Psyllid ID: psy10283

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------6
Protein Sequence
MLPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER
Secondary Structure (PSIPRED)
ccccccEEccccccccccEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHccccccccEEEEHHccccccHHHHHHHHcccccEEEEEEEEccccccccc
Coil and Loop (DISEMBL)
mlpldliwnctplppdkklFVGMLSkqqneddvrkifapfgtieectvlkgpdgtsker
Flexible Loop (DISEMBL)
MLPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFapfgtieectvlkgpdgtsker
Low Complexity Region (SEG)
MLPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER
Disordered region (IsUnstruct)
***LDLIWNCTPLPPDKKLFVGMLSKQ**EDDVRKIFAPFGTIEECTVL**********
Disordered Region (DISOPRED)
***L*********PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV****D******
Disordered Region (DISEMBL)
MLPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG********
Disordered Region (DISPRO)
MLPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER
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	59	2.2.26 [Sep-21-2011]
Q8CIN6	465	CUGBP Elav-like family me	yes	N/A	0.711	0.090	0.785	6e-14
Q5SZQ8	465	CUGBP Elav-like family me	no	N/A	0.711	0.090	0.785	6e-14
Q08E07	461	CUGBP Elav-like family me	yes	N/A	0.711	0.091	0.785	6e-14
Q5NVC8	486	CUGBP Elav-like family me	no	N/A	0.830	0.100	0.666	1e-13
Q9BZC1	486	CUGBP Elav-like family me	no	N/A	0.830	0.100	0.666	1e-13
Q7TSY6	486	CUGBP Elav-like family me	no	N/A	0.830	0.100	0.666	1e-13
Q91579	462	CUGBP Elav-like family me	N/A	N/A	0.711	0.090	0.738	2e-13
Q6DGV1	520	CUGBP Elav-like family me	no	N/A	0.711	0.080	0.738	4e-13
Q4R535	474	CUGBP Elav-like family me	N/A	N/A	0.711	0.088	0.738	5e-13
Q7TN33	460	CUGBP Elav-like family me	no	N/A	0.711	0.091	0.761	5e-13

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

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|Q5SZQ8|CELF3_HUMAN CUGBP Elav-like family member 3 OS=Homo sapiens GN=CELF3 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|Q08E07|CELF3_BOVIN CUGBP Elav-like family member 3 OS=Bos taurus GN=CELF3 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|Q5NVC8|CELF4_PONAB CUGBP Elav-like family member 4 OS=Pongo abelii GN=CELF4 PE=2 SV=2

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 9   NCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           +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 = 74.7 bits (182), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 9   NCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           +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|Q7TSY6|CELF4_MOUSE CUGBP Elav-like family member 4 OS=Mus musculus GN=Celf4 PE=1 SV=2

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 9   NCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           +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 = 74.3 bits (181), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|Q6DGV1|CELF4_DANRE CUGBP Elav-like family member 4 OS=Danio rerio GN=celf4 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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)

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

 Score = 72.8 bits (177), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|Q7TN33|CELF6_MOUSE CUGBP Elav-like family member 6 OS=Mus musculus GN=Celf6 PE=2 SV=1

 Score = 72.8 bits (177), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 32/42 (76%), Positives = 37/42 (88%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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)

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	59
270016805	214	hypothetical protein TcasGA2_TC001521 [T	0.711	0.196	0.809	5e-14
269868259	154	Bruno-3 transcript variant 32 [Drosophil	0.728	0.279	0.813	2e-13
357623708	260	hypothetical protein KGM_06212 [Danaus p	0.728	0.165	0.767	2e-13
189241911	569	PREDICTED: similar to bruno-3 CG12478-PA	0.711	0.073	0.809	2e-13
37588904	291	TNRC4 protein, partial [Homo sapiens]	0.711	0.144	0.785	2e-13
195427147	645	GK17101 [Drosophila willistoni] gi|19415	0.711	0.065	0.833	3e-13
269868210	370	Bruno-3 transcript variant 9, partial [D	0.711	0.113	0.833	4e-13
269868212	370	Bruno-3 transcript variant 9, partial [D	0.711	0.113	0.833	4e-13
269868303	407	Bruno-3 transcript variant 4 [Drosophila	0.711	0.103	0.833	4e-13
149030745	284	similar to trinucleotide repeat containi	0.711	0.147	0.785	4e-13

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

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 34/42 (80%), Positives = 40/42 (95%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|269868259|gb|ACZ52434.1| Bruno-3 transcript variant 32 [Drosophila melanogaster]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 40/43 (93%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          D+KLFVGMLSKQQ EDDVR+IF PFGTIEECT+L+GPDG SK+
Sbjct: 23 DRKLFVGMLSKQQTEDDVRQIFHPFGTIEECTILRGPDGASKD 65

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357623708|gb|EHJ74752.1| hypothetical protein KGM_06212 [Danaus plexippus]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/43 (76%), Positives = 40/43 (93%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          D+KLFVGMLSKQQ E+DVR++F PFGTIEEC++L+GPDG SKE
Sbjct: 37 DRKLFVGMLSKQQTEEDVRQLFTPFGTIEECSILRGPDGASKE 79

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 79.3 bits (194), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 34/42 (80%), Positives = 40/42 (95%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|37588904|gb|AAH04145.2| TNRC4 protein, partial [Homo sapiens]

 Score = 79.3 bits (194), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 85  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 126

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|195427147|ref|XP_002061640.1| GK17101 [Drosophila willistoni] gi|194157725|gb|EDW72626.1| GK17101 [Drosophila willistoni]

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

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           D+KLFVGMLSKQQ EDDVR+IF PFGTIEECT+L+GPDG SK
Sbjct: 88  DRKLFVGMLSKQQTEDDVRQIFQPFGTIEECTILRGPDGASK 129

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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|269868212|gb|ACZ52412.1| Bruno-3 transcript variant 9, partial [Drosophila pseudoobscura]

 Score = 78.6 bits (192), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/42 (83%), Positives = 40/42 (95%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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 = 78.6 bits (192), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/42 (83%), Positives = 40/42 (95%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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

>gi|149030745|gb|EDL85782.1| similar to trinucleotide repeat containing 4 (predicted), isoform CRA_b [Rattus norvegicus]

 Score = 78.6 bits (192), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 94  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

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	59
UNIPROTKB|A1L544	139	TNRC4 "Trinucleotide repeat co	0.711	0.302	0.785	1.8e-14
FB|FBgn0264001	422	bru-3 "bruno-3" [Drosophila me	0.711	0.099	0.833	2.1e-14
UNIPROTKB|K7EJK3	162	CELF4 "CUGBP Elav-like family	0.830	0.302	0.666	2.3e-14
UNIPROTKB|F1NXF6	476	BRUNOL6 "Uncharacterized prote	0.762	0.094	0.760	2.8e-14
UNIPROTKB|Q5SZQ7	415	CELF3 "CUGBP Elav-like family	0.711	0.101	0.785	9e-14
UNIPROTKB|F1NYP4	361	CELF4 "Uncharacterized protein	0.762	0.124	0.711	1e-13
UNIPROTKB|Q08E07	461	CELF3 "CUGBP Elav-like family	0.711	0.091	0.785	1.2e-13
UNIPROTKB|Q5SZQ8	465	CELF3 "CUGBP Elav-like family	0.711	0.090	0.785	1.2e-13
UNIPROTKB|F1ST15	465	CELF3 "Uncharacterized protein	0.711	0.090	0.785	1.2e-13
MGI|MGI:1926034	465	Celf3 "CUGBP, Elav-like family	0.711	0.090	0.785	1.2e-13

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

 Score = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             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

FB|FBgn0264001 bru-3 "bruno-3" [Drosophila melanogaster (taxid:7227)]

 Score = 191 (72.3 bits), Expect = 2.1e-14, P = 2.1e-14
 Identities = 35/42 (83%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             D+KLFVGMLSKQQ EDDVR+IF PFGTIEECT+L+GPDG SK
Sbjct:    54 DRKLFVGMLSKQQTEDDVRQIFHPFGTIEECTILRGPDGASK 95

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IDA

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

GO:0043234 "protein complex" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

UNIPROTKB|K7EJK3 CELF4 "CUGBP Elav-like family member 4" [Homo sapiens (taxid:9606)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query:     9 NCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             +C   PP  D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct:    19 SCLRQPPSQDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 69

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 191 (72.3 bits), Expect = 2.8e-14, P = 2.8e-14
 Identities = 35/46 (76%), Positives = 41/46 (89%)

Query:    13 LPP-DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             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 = 9.0e-14, P = 9.0e-14
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             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|F1NYP4 CELF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 183 (69.5 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 32/45 (71%), Positives = 40/45 (88%)

Query:    13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             +P D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct:     5 VPEDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 49

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 = 1.2e-13, P = 1.2e-13
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             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 = 1.2e-13, P = 1.2e-13
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             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

UNIPROTKB|F1ST15 CELF3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 185 (70.2 bits), Expect = 1.2e-13, P = 1.2e-13
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    95 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 136

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

GO:0030317 "sperm motility" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 185 (70.2 bits), Expect = 1.2e-13, P = 1.2e-13
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             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

---

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	0.7118	0.0911	yes	N/A
Q8CIN6	CELF3_MOUSE	No assigned EC number	0.7857	0.7118	0.0903	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	59
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	6e-28
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-19
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	5e-17
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-17
smart00360	73	smart00360, RRM, RNA recognition motif	3e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-07
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-07
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-06
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-06
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	6e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	9e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	8e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	8e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	9e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	6e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	8e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	0.001
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.001
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.001
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.001
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.002
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.002
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.002
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.002
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.002
cd12623	91	cd12623, RRM_PPARGC1A, RNA recognition motif in pe	0.003
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.003
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.003
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.003
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.004
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	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 = 94.8 bits (236), Expect = 6e-28
 Identities = 34/42 (80%), Positives = 39/42 (92%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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 = 73.7 bits (181), Expect = 1e-19
 Identities = 28/42 (66%), Positives = 37/42 (88%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          ++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 = 67.0 bits (163), Expect = 5e-17
 Identities = 26/42 (61%), Positives = 37/42 (88%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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 = 66.8 bits (164), Expect = 6e-17
 Identities = 21/41 (51%), Positives = 27/41 (65%), Gaps = 1/41 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          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 = 44.5 bits (106), Expect = 3e-08
 Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           LFVG L     E+++R++F+ FG +E   +++  + G SK
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSK 41

Length = 73

>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 = 44.1 bits (105), Expect = 4e-08
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|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 = 43.0 bits (102), Expect = 2e-07
 Identities = 14/35 (40%), Positives = 22/35 (62%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 42.7 bits (101), Expect = 2e-07
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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 = 42.7 bits (101), Expect = 2e-07
 Identities = 20/45 (44%), Positives = 30/45 (66%), Gaps = 3/45 (6%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          PP+ +LF+ +  K   EDD+R+ FAPFG I++  V+K  D  +KE
Sbjct: 1  PPNSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVK--DKQTKE 42

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|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 = 42.0 bits (99), Expect = 5e-07
 Identities = 17/33 (51%), Positives = 21/33 (63%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 40.3 bits (95), Expect = 2e-06
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 40.4 bits (95), Expect = 2e-06
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 56
          ++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 = 39.2 bits (92), Expect = 4e-06
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          +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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 38.9 bits (91), Expect = 5e-06
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          +FVG LS + + + +R  FAPFG I +  V+K    T K +
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQ-TGKSK 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|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 = 39.0 bits (91), Expect = 6e-06
 Identities = 11/33 (33%), Positives = 22/33 (66%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 38.3 bits (90), Expect = 7e-06
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 38.8 bits (91), Expect = 7e-06
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 38.4 bits (90), Expect = 8e-06
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.5 bits (90), Expect = 9e-06
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT 55
          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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.9 bits (88), Expect = 1e-05
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 38.4 bits (90), Expect = 1e-05
 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG-PDGTSK 57
           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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 37.7 bits (88), Expect = 2e-05
 Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          KLF+G LS +  +D ++  F+ +G I +C V+K P+ T + R
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPN-TKRSR 41

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

 Score = 37.8 bits (87), Expect = 2e-05
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          +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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.5 bits (87), Expect = 2e-05
 Identities = 9/33 (27%), Positives = 22/33 (66%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 37.6 bits (88), Expect = 2e-05
 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.1 bits (86), Expect = 2e-05
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 37.5 bits (87), Expect = 2e-05
 Identities = 14/33 (42%), Positives = 25/33 (75%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 37.0 bits (85), Expect = 3e-05
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 36.9 bits (86), Expect = 3e-05
 Identities = 12/32 (37%), Positives = 21/32 (65%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 49
          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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 36.8 bits (86), Expect = 3e-05
 Identities = 14/40 (35%), Positives = 22/40 (55%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.0 bits (86), Expect = 4e-05
 Identities = 16/33 (48%), Positives = 21/33 (63%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 49
          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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.7 bits (85), Expect = 4e-05
 Identities = 13/35 (37%), Positives = 22/35 (62%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 38.0 bits (88), Expect = 5e-05
 Identities = 16/41 (39%), Positives = 24/41 (58%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
           P   KL+VG L     E ++R+IF PFG IE+  + + P+ 
Sbjct: 184 PNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPET 224

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|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 = 36.4 bits (84), Expect = 6e-05
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          KLF+G LS   NE  + ++F+ +G I E  V+K  + T + R
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSR 42

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

 Score = 36.2 bits (83), Expect = 8e-05
 Identities = 16/43 (37%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          +KLF+G LS +  +D +R+ F  +GT+ +C V++ P  T + R
Sbjct: 3  RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQ-TKRSR 44

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

 Score = 35.8 bits (83), Expect = 8e-05
 Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 3/41 (7%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          +LFV ++ K   E+D+R+ F  FG IE  +++K  D  + E
Sbjct: 3  RLFV-VIPKSYTEEDLREKFKEFGDIEYVSIVK--DKNTGE 40

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|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 = 35.7 bits (83), Expect = 9e-05
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTI 43
          +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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 35.5 bits (82), Expect = 1e-04
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          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|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 = 1e-04
 Identities = 14/37 (37%), Positives = 23/37 (62%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 35.4 bits (81), Expect = 1e-04
 Identities = 14/35 (40%), Positives = 24/35 (68%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 35.2 bits (82), Expect = 1e-04
 Identities = 11/40 (27%), Positives = 21/40 (52%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          L+V  L     E+D+R+ F+P+G +E   +++  D     
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGF 40

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

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 35.6 bits (82), Expect = 1e-04
 Identities = 15/40 (37%), Positives = 27/40 (67%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          ++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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 35.4 bits (82), Expect = 1e-04
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 35.5 bits (81), Expect = 2e-04
 Identities = 12/36 (33%), Positives = 23/36 (63%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          +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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 34.9 bits (81), Expect = 2e-04
 Identities = 10/34 (29%), Positives = 20/34 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          +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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 35.0 bits (80), Expect = 2e-04
 Identities = 13/37 (35%), Positives = 25/37 (67%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
          +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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 34.7 bits (80), Expect = 2e-04
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          +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|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 = 5e-04
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          +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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 33.7 bits (77), Expect = 5e-04
 Identities = 11/34 (32%), Positives = 22/34 (64%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
          +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|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 = 33.7 bits (78), Expect = 6e-04
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          ++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|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 = 8e-04
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
          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|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 33.5 bits (77), Expect = 8e-04
 Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           +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

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

 Score = 33.3 bits (77), Expect = 0.001
 Identities = 10/39 (25%), Positives = 23/39 (58%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          ++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|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 = 33.1 bits (76), Expect = 0.001
 Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 1/36 (2%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
          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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 33.4 bits (77), Expect = 0.001
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIE 44
          +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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 32.7 bits (75), Expect = 0.001
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          +LFV  L     E+++R++F  FG I E 
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEV 29

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

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

 Score = 34.2 bits (77), Expect = 0.002
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
             +  LFVG L     E+D+R++F  FG ++   +
Sbjct: 113 EENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRL 147

Length = 306

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

 Score = 32.2 bits (74), Expect = 0.002
 Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP-DGTSK 57
          L VG L  +  ++  R++ +PFG +E C ++     G SK
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESK 41

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

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

 Score = 32.4 bits (74), Expect = 0.002
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 56
          + 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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 32.3 bits (73), Expect = 0.002
 Identities = 14/30 (46%), Positives = 20/30 (66%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIE 44
          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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 32.2 bits (74), Expect = 0.002
 Identities = 11/40 (27%), Positives = 24/40 (60%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          ++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|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins

 Score = 32.2 bits (73), Expect = 0.003
 Identities = 15/38 (39%), Positives = 20/38 (52%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 56
          ++VG +       ++R  F  FG IEECTV    DG S
Sbjct: 5  IYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRDDGDS 42

This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA. . Length = 91

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 31.8 bits (73), Expect = 0.003
 Identities = 11/41 (26%), Positives = 24/41 (58%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           KL V  +  +  + ++R++F+PFG ++   + K  DG+ +
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHR 41

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 32.0 bits (73), Expect = 0.003
 Identities = 11/30 (36%), Positives = 20/30 (66%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECT 47
          +++VG +S +  ED +R+ F+PFG I+   
Sbjct: 2  RVYVGSISFELGEDTIRQAFSPFGPIKSID 31

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

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

 Score = 32.2 bits (73), Expect = 0.003
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          KLFVG L     E D+ + F+ FG +E+  V+     T K+R
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQ-TGKKR 41

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 31.6 bits (72), Expect = 0.004
 Identities = 7/31 (22%), Positives = 15/31 (48%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 49
          ++ G         DV+++F   G + + T+L
Sbjct: 2  VYAGPFPTSFCLSDVKRLFETCGPVRKVTML 32

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 31.5 bits (71), Expect = 0.004
 Identities = 13/36 (36%), Positives = 22/36 (61%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
          K+FVG LS   ++ D++  F  FG + +CT+   P+
Sbjct: 1  KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPN 36

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	59
KOG0144|consensus	510		99.45
KOG0149|consensus	247		99.44
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.4
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.35
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.32
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.31
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.3
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.27
KOG0126|consensus	219		99.25
KOG0117|consensus	506		99.2
KOG0148|consensus	321		99.17
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.14
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.1
KOG0113|consensus	335		99.07
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.07
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.06
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.06
PLN03120	260	nucleic acid binding protein; Provisional	99.05
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.04
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.04
KOG0144|consensus	510		99.01
PLN03121	243	nucleic acid binding protein; Provisional	98.99
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.98
KOG0145|consensus	360		98.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.97
KOG0127|consensus	678		98.96
KOG4205|consensus	311		98.96
KOG0148|consensus	321		98.96
KOG0125|consensus	376		98.94
KOG0121|consensus	153		98.92
KOG0146|consensus	371		98.9
KOG0109|consensus	346		98.9
KOG0123|consensus	369		98.9
KOG0114|consensus	124		98.88
PLN03213	759	repressor of silencing 3; Provisional	98.88
KOG0122|consensus	270		98.86
KOG0131|consensus	203		98.83
smart00362	72	RRM_2 RNA recognition motif.	98.8
KOG0117|consensus	506		98.8
KOG0107|consensus	195		98.71
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.7
KOG0108|consensus	435		98.68
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.67
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.66
KOG0105|consensus	241		98.63
KOG0145|consensus	360		98.61
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.6
smart00360	71	RRM RNA recognition motif.	98.58
KOG0147|consensus	549		98.58
KOG1548|consensus	382		98.53
KOG0124|consensus	544		98.52
KOG0109|consensus	346		98.51
KOG0131|consensus	203		98.5
KOG4205|consensus	311		98.49
KOG0533|consensus	243		98.49
KOG4207|consensus	256		98.45
KOG0111|consensus	298		98.41
KOG4212|consensus	608		98.38
KOG0124|consensus	544		98.37
KOG0127|consensus	678		98.35
KOG0146|consensus	371		98.26
KOG4206|consensus	221		98.24
KOG0415|consensus	479		98.16
KOG0123|consensus	369		98.03
KOG0132|consensus	894		97.96
KOG4212|consensus	608		97.93
KOG4454|consensus	267		97.92
KOG0130|consensus	170		97.87
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.87
KOG0151|consensus	877		97.78
KOG4209|consensus	231		97.73
KOG0116|consensus	419		97.72
KOG0153|consensus	377		97.72
KOG0110|consensus	725		97.58
KOG4661|consensus	940		97.58
KOG0147|consensus	549		97.38
KOG0106|consensus	216		97.19
KOG4660|consensus	549		97.17
KOG0226|consensus	290		97.12
KOG0129|consensus	520		97.12
KOG3152|consensus	278		97.09
KOG4208|consensus	214		97.01
KOG0115|consensus	275		96.86
KOG4210|consensus	285		96.85
KOG0128|consensus	881		96.84
KOG0129|consensus	520		96.74
KOG0120|consensus	500		96.65
smart00361	70	RRM_1 RNA recognition motif.	96.62
KOG4849|consensus	498		96.62
KOG1457|consensus	284		96.44
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	96.37
KOG4211|consensus	510		96.24
KOG1190|consensus	492		96.16
KOG0110|consensus	725		96.16
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	95.3
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.23
KOG1855|consensus	484		95.0
KOG1457|consensus	284		94.97
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	94.63
KOG4211|consensus	510		94.6
KOG1995|consensus	351		94.32
KOG0112|consensus	975		93.69
KOG0105|consensus	241		93.64
KOG4206|consensus	221		93.49
KOG4676|consensus	479		93.47
KOG1190|consensus	492		93.19
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	93.15
KOG0128|consensus	881		91.36
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	91.3
PF15513	62	DUF4651: Domain of unknown function (DUF4651)	90.86
KOG0112|consensus	975		88.54
KOG0106|consensus	216		87.42
KOG4454|consensus	267		86.51
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	84.97
COG5175	480	MOT2 Transcriptional repressor [Transcription]	84.85
KOG1456|consensus	494		84.59
KOG2891|consensus	445		83.51
KOG2314|consensus	698		81.77
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	80.23

>KOG0144|consensus

Probab=99.45  E-value=2.4e-14  Score=84.46  Aligned_cols=58  Identities=45%  Similarity=0.805  Sum_probs=54.5

Q ss_pred             CcceeecccCCCCCC---CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          1 MLPLDLIWNCTPLPP---DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         1 ~~~~~~~~~~~~~~~---~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |.|+++.+++.+...   +++||||.|+..++|.+++++|++||.|++|.|++|.+|.+||
T Consensus       106 ~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRG  166 (510)
T KOG0144|consen  106 HHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRG  166 (510)
T ss_pred             CcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccc
Confidence            579999999997765   8999999999999999999999999999999999999999998

>KOG0149|consensus

Probab=99.44  E-value=1.8e-13  Score=75.69  Aligned_cols=44  Identities=34%  Similarity=0.588  Sum_probs=41.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .-.+||||+|++.++.+.|++.|++||+|.++.|+.|+. |+|||
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskG   55 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKG   55 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccc
Confidence            456899999999999999999999999999999999999 99998

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

Probab=99.40  E-value=1.5e-12  Score=68.01  Aligned_cols=44  Identities=32%  Similarity=0.568  Sum_probs=41.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||+.+++++|+++|++||.|.+++++.|+. +++||
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG   77 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRG   77 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcce
Confidence            567899999999999999999999999999999999988 88887

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.35  E-value=3e-12  Score=73.64  Aligned_cols=43  Identities=26%  Similarity=0.597  Sum_probs=40.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+|||+|||..+++++|+++|+.||+|.++++++|+. |+++|
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g   46 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLG   46 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccce
Confidence            57899999999999999999999999999999999987 88887

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

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

Probab=99.32  E-value=6.5e-12  Score=76.86  Aligned_cols=51  Identities=22%  Similarity=0.421  Sum_probs=45.3

Q ss_pred             ccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         8 ~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |...++...++|||+|||.++++++|+++|++||.|.+++|++|..|++||
T Consensus        50 ~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRG  100 (578)
T TIGR01648        50 WSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRG  100 (578)
T ss_pred             ccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccc
Confidence            444455678999999999999999999999999999999999995599987

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.31  E-value=7.5e-12  Score=71.99  Aligned_cols=43  Identities=23%  Similarity=0.470  Sum_probs=40.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...|||+|||+.+++++|+++|++||.|.+++|+.|+. |++||
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG  312 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKG  312 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccc
Confidence            34699999999999999999999999999999999996 99887

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.30  E-value=9.1e-12  Score=72.53  Aligned_cols=56  Identities=23%  Similarity=0.415  Sum_probs=47.4

Q ss_pred             ceeecccCCC--CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          3 PLDLIWNCTP--LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~--~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++++.|+.+.  .....+|||+|||..+++++|+++|++||.|.+++++.|+. |++||
T Consensus       178 ~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG  236 (346)
T TIGR01659       178 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRG  236 (346)
T ss_pred             eeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccce
Confidence            4667776542  23567899999999999999999999999999999999987 88876

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=99.27  E-value=2.4e-11  Score=70.79  Aligned_cols=45  Identities=20%  Similarity=0.461  Sum_probs=42.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||++||.++++++|+++|+.||.|.+++|+.|.. +++||
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srG  150 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFG  150 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCc
Confidence            3578999999999999999999999999999999999987 88887

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).

>KOG0126|consensus

Probab=99.25  E-value=2.1e-12  Score=69.67  Aligned_cols=44  Identities=23%  Similarity=0.502  Sum_probs=42.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+..||||+||+..|+.++-.+|++||+|.++.+++|+. |+|+|
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKG   78 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKG   78 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccc
Confidence            567899999999999999999999999999999999999 99998

>KOG0117|consensus

Probab=99.20  E-value=4e-11  Score=71.32  Aligned_cols=51  Identities=27%  Similarity=0.585  Sum_probs=48.2

Q ss_pred             ccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         8 ~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      |...+++.++.||||.||.++.|++|..+|+..|+|.++++|+|+. |.+||
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRG  126 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRG  126 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcc
Confidence            7777778899999999999999999999999999999999999988 99998

>KOG0148|consensus

Probab=99.17  E-value=4.9e-11  Score=67.51  Aligned_cols=55  Identities=33%  Similarity=0.660  Sum_probs=48.8

Q ss_pred             eeecccCCCCCC-------CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          4 LDLIWNCTPLPP-------DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         4 ~~~~~~~~~~~~-------~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++++|++.|...       -..+|||-|...++.++|++.|.+||+|.+++|++|.. +|+||
T Consensus        43 ~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKG  105 (321)
T KOG0148|consen   43 LKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKG  105 (321)
T ss_pred             hccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccc
Confidence            578899887442       23599999999999999999999999999999999999 99998

>PF00076 RRM_1: RNA recognition motif

Probab=99.16  E-value=4.5e-11  Score=54.70  Aligned_cols=39  Identities=38%  Similarity=0.755  Sum_probs=34.5

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCC
Q psy10283         19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK   57 (59)
Q Consensus        19 l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~r   57 (59)
                      |||+|||..+++++|+++|++||.+..+.+..+..++++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~   39 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSK   39 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccccccccc
Confidence            799999999999999999999999999999987435443

(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 ....

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

Probab=99.14  E-value=1.3e-10  Score=71.66  Aligned_cols=44  Identities=32%  Similarity=0.569  Sum_probs=41.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++||||||++.+++++|+++|+.||.|.++++++|+. |++||
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskG  150 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKG  150 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCC
Confidence            467999999999999999999999999999999999988 99987

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.

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

Probab=99.10  E-value=2.4e-10  Score=69.43  Aligned_cols=56  Identities=25%  Similarity=0.525  Sum_probs=47.1

Q ss_pred             ceeecccCCCCC----CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          3 PLDLIWNCTPLP----PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~~----~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ++++.|+...+.    ...+|||+||+.++++++|+++|+.||.|.+|+++.|..|+++|
T Consensus        71 ~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg  130 (562)
T TIGR01628        71 PIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRG  130 (562)
T ss_pred             eEEeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCccc
Confidence            466777654322    35689999999999999999999999999999999997788887

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

>KOG0113|consensus

Probab=99.07  E-value=2.3e-10  Score=65.46  Aligned_cols=44  Identities=32%  Similarity=0.559  Sum_probs=41.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .-++|||+.|+..++|.+|+..|+.||.|..+.++.|.. |+++|
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskG  144 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKG  144 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccc
Confidence            457999999999999999999999999999999999988 99998

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

Probab=99.07  E-value=4.8e-10  Score=69.18  Aligned_cols=43  Identities=23%  Similarity=0.582  Sum_probs=40.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+||+..+++++|+++|+.||.|.+++++.|+. |++||
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKG  247 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKG  247 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCC
Confidence            46899999999999999999999999999999999988 88887

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.

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

Probab=99.06  E-value=4.8e-10  Score=66.55  Aligned_cols=45  Identities=24%  Similarity=0.428  Sum_probs=41.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.|+. |+++|.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~  133 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGV  133 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceE
Confidence            467899999999999999999999999999999999988 888873

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.06  E-value=4.1e-10  Score=51.89  Aligned_cols=40  Identities=30%  Similarity=0.697  Sum_probs=33.7

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        19 l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |||+|||+.+++++|.++|+.+|.|..+.+..+++|.++|
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~   40 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRG   40 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCC
Confidence            7999999999999999999999999999999986655443

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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.05  E-value=5e-10  Score=63.17  Aligned_cols=38  Identities=21%  Similarity=0.297  Sum_probs=35.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      .++|||+||++.+++++|+++|+.||.|.++.++.|..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~   41 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE   41 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC
Confidence            57899999999999999999999999999999998864

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

Probab=99.04  E-value=9.1e-10  Score=66.02  Aligned_cols=44  Identities=23%  Similarity=0.550  Sum_probs=40.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...+|||+|||..+++++|+++|+.||.|..+.++.+.. |+++|
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g  338 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKG  338 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCe
Confidence            357899999999999999999999999999999999987 88887

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

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

Probab=99.04  E-value=5.3e-10  Score=67.95  Aligned_cols=41  Identities=27%  Similarity=0.453  Sum_probs=39.1

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .|||||||.++++++|+++|+.||.|.++++.+|.. ++++|
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G   43 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLG   43 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcce
Confidence            699999999999999999999999999999999988 88887

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

>KOG0144|consensus

Probab=99.01  E-value=4.6e-10  Score=66.76  Aligned_cols=46  Identities=33%  Similarity=0.601  Sum_probs=42.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+.-++|||.+|+..+|.+|+++|++||.|.+|.|++|+. |.++|
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~g   77 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKG   77 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccc
Confidence            33566899999999999999999999999999999999998 88877

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.99  E-value=1.5e-09  Score=60.67  Aligned_cols=39  Identities=26%  Similarity=0.362  Sum_probs=36.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ...+|||+||++.+++++|+++|+.||+|.+++++.|..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e   42 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE   42 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC
Confidence            457899999999999999999999999999999998854

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

Probab=98.98  E-value=1.7e-09  Score=58.92  Aligned_cols=44  Identities=30%  Similarity=0.649  Sum_probs=40.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      ..+|||+|||..+++++|+++|..||.+..+.+..|+. |+++|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~  159 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGF  159 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCce
Confidence            48999999999999999999999999999999999976 888873

>KOG0145|consensus

Probab=98.97  E-value=2.7e-10  Score=64.60  Aligned_cols=56  Identities=25%  Similarity=0.467  Sum_probs=49.6

Q ss_pred             ceeecccCCCCC--CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          3 PLDLIWNCTPLP--PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~~--~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+|++++.+...  .+.+|||.+||..++..+|+.+|++||.|..-+|+.|.- |.+||
T Consensus       112 TIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srG  170 (360)
T KOG0145|consen  112 TIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRG  170 (360)
T ss_pred             eEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecc
Confidence            478888887544  678999999999999999999999999999999999987 88887

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

Probab=98.97  E-value=1.9e-09  Score=64.06  Aligned_cols=43  Identities=42%  Similarity=0.736  Sum_probs=40.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|++||.|..+.++.+.. |+++|
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g  229 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKG  229 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccce
Confidence            57899999999999999999999999999999999988 78876

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.

>KOG0127|consensus

Probab=98.96  E-value=1.5e-09  Score=66.24  Aligned_cols=44  Identities=30%  Similarity=0.551  Sum_probs=41.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...+|||.|||++++++.|...|++||+|..+.++.++. |+++|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skG  335 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKG  335 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCccc
Confidence            457899999999999999999999999999999999999 99988

>KOG4205|consensus

Probab=98.96  E-value=1.7e-09  Score=62.41  Aligned_cols=44  Identities=36%  Similarity=0.789  Sum_probs=42.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+++|||+|++.++++.|++.|++||+|.+|.+++|+. +++||
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrg   49 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRG   49 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCccc
Confidence            678999999999999999999999999999999999999 88887

>KOG0148|consensus

Probab=98.96  E-value=2.2e-09  Score=60.96  Aligned_cols=38  Identities=34%  Similarity=0.674  Sum_probs=35.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .++.|||||++..++++.+++.|++||.|.++++.+|+
T Consensus       163 ~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q  200 (321)
T KOG0148|consen  163 DNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ  200 (321)
T ss_pred             CCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc
Confidence            57899999999999999999999999999999998886

>KOG0125|consensus

Probab=98.94  E-value=2.1e-09  Score=62.29  Aligned_cols=41  Identities=20%  Similarity=0.388  Sum_probs=37.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ....++|+|+|+||+..+.||+..|++||+|.++.|+++..
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNER  133 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNER  133 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccC
Confidence            34678999999999999999999999999999999999864

>KOG0121|consensus

Probab=98.92  E-value=1.4e-09  Score=56.08  Aligned_cols=39  Identities=21%  Similarity=0.278  Sum_probs=35.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      .+++||||||++.++|+.+.++|+.+|.|..+.+-.|+.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~   73 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRF   73 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccC
Confidence            578999999999999999999999999999987777765

>KOG0146|consensus

Probab=98.90  E-value=1.5e-09  Score=61.77  Aligned_cols=56  Identities=61%  Similarity=0.997  Sum_probs=47.4

Q ss_pred             ceeecccCC--CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          3 PLDLIWNCT--PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~--~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |+++.-+.+  ...++++||||-|...-+|++.+.+|..||.|++|.+.+.++|.+||
T Consensus         4 piqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKG   61 (371)
T KOG0146|consen    4 PIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKG   61 (371)
T ss_pred             CccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCC
Confidence            344444443  34478999999999999999999999999999999999999999887

>KOG0109|consensus

Probab=98.90  E-value=1.1e-09  Score=62.61  Aligned_cols=35  Identities=34%  Similarity=0.840  Sum_probs=33.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .++||||||..+++.+|+.+|++||+|.+|.|+++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN   37 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN   37 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc
Confidence            47999999999999999999999999999999876

>KOG0123|consensus

Probab=98.90  E-value=3.1e-09  Score=62.55  Aligned_cols=52  Identities=25%  Similarity=0.575  Sum_probs=45.7

Q ss_pred             ceeecccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          3 PLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |+++.|+...+..   +||.||+..++..+|.+.|+.||+|.+|+++.|.+| ++|
T Consensus        66 ~~rim~s~rd~~~---~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg  117 (369)
T KOG0123|consen   66 PIRIMWSQRDPSL---VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKG  117 (369)
T ss_pred             EEEeehhccCCce---eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-cee
Confidence            6778888875544   999999999999999999999999999999999877 554

>KOG0114|consensus

Probab=98.88  E-value=7.2e-09  Score=51.86  Aligned_cols=42  Identities=17%  Similarity=0.407  Sum_probs=37.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ++...+-|||.|||+.+|.++..++|..||.|..+++-.+++
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~   55 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE   55 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC
Confidence            455677899999999999999999999999999999876654

>PLN03213 repressor of silencing 3; Provisional

Probab=98.88  E-value=5.7e-09  Score=63.48  Aligned_cols=38  Identities=32%  Similarity=0.573  Sum_probs=34.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ....+||||||++.+++++|+.+|+.||.|.++.|+++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE   45 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT   45 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc
Confidence            35679999999999999999999999999999999944

>KOG0122|consensus

Probab=98.86  E-value=5.8e-09  Score=58.45  Aligned_cols=44  Identities=32%  Similarity=0.551  Sum_probs=41.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +...|-|.||+.++++++|+++|.+||.|.++.+.+|+. |.+||
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kG  232 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKG  232 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccc
Confidence            455799999999999999999999999999999999999 99998

>KOG0131|consensus

Probab=98.83  E-value=3.2e-09  Score=57.35  Aligned_cols=56  Identities=27%  Similarity=0.491  Sum_probs=46.4

Q ss_pred             ceeecccCC---CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEE-EEEeCCC-CCCCC
Q psy10283          3 PLDLIWNCT---PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD-GTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~---~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~-~v~~d~~-g~~rG   58 (59)
                      |++++.++.   ....+.++||+||.+.+++..|.+.|+.||.+.+. ++++|++ |.++|
T Consensus        80 pIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~  140 (203)
T KOG0131|consen   80 PIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKG  140 (203)
T ss_pred             eeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCC
Confidence            678888873   22356799999999999999999999999998774 7888888 77775

>smart00362 RRM_2 RNA recognition motif

Probab=98.80  E-value=2.4e-08  Score=44.98  Aligned_cols=39  Identities=41%  Similarity=0.748  Sum_probs=34.3

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK   57 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~r   57 (59)
                      +|||+|||..+++++++++|++||.+..+.+..+. +.++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~   39 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSK   39 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCC
Confidence            48999999999999999999999999999988776 4443

>KOG0117|consensus

Probab=98.80  E-value=5.5e-09  Score=62.44  Aligned_cols=48  Identities=23%  Similarity=0.435  Sum_probs=41.6

Q ss_pred             eeecccCCCCC-------CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283          4 LDLIWNCTPLP-------PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus         4 ~~~~~~~~~~~-------~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      +.|.||.+...       ..+-|||.||+.++|++.|+++|++||.|++++.++|
T Consensus       240 ~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD  294 (506)
T KOG0117|consen  240 ITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD  294 (506)
T ss_pred             ceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc
Confidence            56889988543       3457999999999999999999999999999988776

>KOG0107|consensus

Probab=98.71  E-value=3.7e-08  Score=53.06  Aligned_cols=38  Identities=21%  Similarity=0.568  Sum_probs=35.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++||||||+..+++.+|+.+|..||.+..+.|...+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP   46 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP   46 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC
Confidence            47899999999999999999999999999999887765

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

Probab=98.70  E-value=3.6e-08  Score=59.45  Aligned_cols=37  Identities=24%  Similarity=0.406  Sum_probs=34.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ++.|||+|||..+++++|+++|++||.|.++.++.++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k   38 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGK   38 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCC
Confidence            5689999999999999999999999999999988653

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).

>KOG0108|consensus

Probab=98.68  E-value=3.2e-08  Score=59.34  Aligned_cols=42  Identities=21%  Similarity=0.446  Sum_probs=41.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +.+||||+|++++++.|.++|+..|.|.+++++.|++ |++||
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G   61 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKG   61 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCc
Confidence            8899999999999999999999999999999999999 99998

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

Probab=98.67  E-value=7.8e-08  Score=58.04  Aligned_cols=38  Identities=26%  Similarity=0.489  Sum_probs=35.0

Q ss_pred             CCCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..+.|||+||+. .+++++|+++|+.||.|.++++++++
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~  312 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK  312 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC
Confidence            467999999998 69999999999999999999999875

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).

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

Probab=98.66  E-value=7.2e-08  Score=59.51  Aligned_cols=49  Identities=22%  Similarity=0.381  Sum_probs=39.8

Q ss_pred             ceeecccCCCCC-------CCCeEEEcCCCCCCcHHHHHHhhccC--CCeEEEEEEeC
Q psy10283          3 PLDLIWNCTPLP-------PDKKLFVGMLSKQQNEDDVRKIFAPF--GTIEECTVLKG   51 (59)
Q Consensus         3 ~~~~~~~~~~~~-------~~~~l~v~~L~~~~~~~~l~~~F~~~--G~i~~~~v~~d   51 (59)
                      .+.++|+.+...       ..++|||+||+..+++++|+++|+.|  |.|.+++++++
T Consensus       213 ~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg  270 (578)
T TIGR01648       213 VIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD  270 (578)
T ss_pred             eEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC
Confidence            356777765321       34679999999999999999999999  99999987654

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.

>KOG0105|consensus

Probab=98.63  E-value=3.6e-08  Score=53.76  Aligned_cols=36  Identities=22%  Similarity=0.555  Sum_probs=32.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      ..+++||||||.++.+.+++++|.+||.|.++.+..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~   40 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKN   40 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEecc
Confidence            578999999999999999999999999999987643

>KOG0145|consensus

Probab=98.61  E-value=9.2e-08  Score=54.52  Aligned_cols=44  Identities=27%  Similarity=0.589  Sum_probs=40.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...+|.|..||..+++++++.+|+..|+|++|++++|+- |++-|
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLG   84 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLG   84 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccc
Confidence            356799999999999999999999999999999999997 87765

>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=98.60  E-value=2.5e-07  Score=41.76  Aligned_cols=37  Identities=35%  Similarity=0.745  Sum_probs=33.7

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG   54 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g   54 (59)
                      +++|++||..+++++++++|+.+|.+..+.+..++.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~   37 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT   37 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC
Confidence            4899999999999999999999999999999887654

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).

>smart00360 RRM RNA recognition motif

Probab=98.58  E-value=1.6e-07  Score=42.00  Aligned_cols=38  Identities=37%  Similarity=0.716  Sum_probs=33.7

Q ss_pred             EcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         21 VGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        21 v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      |+|||..+++++|+++|++||.+..+.+..++. ++++|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~   39 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKG   39 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCc
Confidence            578999999999999999999999999998876 66665

>KOG0147|consensus

Probab=98.58  E-value=4e-08  Score=59.76  Aligned_cols=42  Identities=43%  Similarity=0.680  Sum_probs=39.5

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      ++|||||.+++++++|+.+|++||.|+.+.+++|.+ |+++|.
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgf  322 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGF  322 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCc
Confidence            499999999999999999999999999999999986 999883

>KOG1548|consensus

Probab=98.53  E-value=3.6e-07  Score=53.48  Aligned_cols=51  Identities=16%  Similarity=0.304  Sum_probs=42.1

Q ss_pred             ccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEE--------EEEEeCCCCCCCC
Q psy10283          8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPDGTSKE   58 (59)
Q Consensus         8 ~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~--------~~v~~d~~g~~rG   58 (59)
                      |....+..+..|||.|||.++|.+++.++|+.||-|.+        |++.++.+|+.||
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKG  184 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKG  184 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccC
Confidence            44444456778999999999999999999999998766        7778887788877

>KOG0124|consensus

Probab=98.52  E-value=5.4e-08  Score=57.57  Aligned_cols=43  Identities=33%  Similarity=0.602  Sum_probs=41.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      -|++|||.+.+...++.++..|.+||+|.++.+.+|+. +++||
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKg  156 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKG  156 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccc
Confidence            47899999999999999999999999999999999998 99987

>KOG0109|consensus

Probab=98.51  E-value=1.2e-07  Score=54.47  Aligned_cols=48  Identities=23%  Similarity=0.415  Sum_probs=39.8

Q ss_pred             eecccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283          5 DLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus         5 ~~~~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ++..+.+-.....+++|||+.+.++..+++..|++||.+.+|++++|-
T Consensus        67 nVeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy  114 (346)
T KOG0109|consen   67 NVEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDY  114 (346)
T ss_pred             EEEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecce
Confidence            344444444467899999999999999999999999999999998773

>KOG0131|consensus

Probab=98.50  E-value=1.3e-07  Score=51.33  Aligned_cols=47  Identities=19%  Similarity=0.292  Sum_probs=41.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +.....+||||||+..++++.|.++|-+.|+|.++++++|+. ..++|
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qG   52 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQG   52 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccc
Confidence            345678999999999999999999999999999999999987 65555

>KOG4205|consensus

Probab=98.49  E-value=3e-07  Score=53.28  Aligned_cols=43  Identities=26%  Similarity=0.571  Sum_probs=40.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+++|||.||..++++++++.|++||.|.++.++.|.. .++||
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rg  140 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRG  140 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeeccccccccc
Confidence            45899999999999999999999999999999999998 87776

>KOG0533|consensus

Probab=98.49  E-value=3.1e-07  Score=51.66  Aligned_cols=45  Identities=24%  Similarity=0.350  Sum_probs=41.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER   59 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG~   59 (59)
                      ...+++|.|||+.+.+++|+++|..||.+..+-+-.|+.|++.|+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gt  126 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGT  126 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCcc
Confidence            347899999999999999999999999999999999988988875

>KOG4207|consensus

Probab=98.45  E-value=2.7e-07  Score=51.06  Aligned_cols=44  Identities=20%  Similarity=0.369  Sum_probs=40.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....|-|-||.+.++.++|+.+|++||.|.+|.|+.|+. +.++|
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRg   56 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRG   56 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccc
Confidence            456788999999999999999999999999999999998 88887

>KOG0111|consensus

Probab=98.41  E-value=1.3e-07  Score=52.77  Aligned_cols=45  Identities=22%  Similarity=0.445  Sum_probs=42.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++||||+|...+++.-|...|-+||.|.++.++.|.+ +++||
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRg   53 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRG   53 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccc
Confidence            4578899999999999999999999999999999999988 89887

>KOG4212|consensus

Probab=98.38  E-value=7.8e-07  Score=53.72  Aligned_cols=44  Identities=16%  Similarity=0.354  Sum_probs=40.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhc-cCCCeEEEEEEeCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFA-PFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~-~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..+.+||.|+|++..|.+|+++|. .-|+|+-|.+++|..||+||
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rG   87 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARG   87 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCC
Confidence            345699999999999999999995 68999999999999999997

>KOG0124|consensus

Probab=98.37  E-value=7.9e-07  Score=52.79  Aligned_cols=43  Identities=23%  Similarity=0.582  Sum_probs=39.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      -.++||..+..+.++++++.+|+.||+|..|.+.+++. +.+||
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkG  253 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKG  253 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccc
Confidence            35899999999999999999999999999999999998 77776

>KOG0127|consensus

Probab=98.35  E-value=8.9e-07  Score=54.50  Aligned_cols=43  Identities=19%  Similarity=0.369  Sum_probs=40.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +.+|||++||++++.++|.++|+.+|+|..+.++.+.. +.+||
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RG   48 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRG   48 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccC
Confidence            37899999999999999999999999999999999988 77777

>KOG0146|consensus

Probab=98.26  E-value=1.7e-06  Score=49.60  Aligned_cols=45  Identities=27%  Similarity=0.456  Sum_probs=41.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK   57 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~r   57 (59)
                      .+++|+|||..||.+..+.+|-..|-+||.|.+.++..|+. +.+|
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSK  327 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSK  327 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhcccccc
Confidence            34789999999999999999999999999999999999987 6665

>KOG4206|consensus

Probab=98.24  E-value=3e-06  Score=47.04  Aligned_cols=42  Identities=19%  Similarity=0.535  Sum_probs=34.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHH----hhccCCCeEEEEEEeCCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGPDGTSKER   59 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~----~F~~~G~i~~~~v~~d~~g~~rG~   59 (59)
                      ..++||.||+..+..++|+.    +|++||+|.++.....  .+.|||
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt--~KmRGQ   54 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT--PKMRGQ   54 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC--CCccCc
Confidence            34999999999999988877    9999999999876544  456664

>KOG0415|consensus

Probab=98.16  E-value=2.4e-06  Score=50.54  Aligned_cols=42  Identities=36%  Similarity=0.714  Sum_probs=38.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS   56 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~   56 (59)
                      ...-|||..|.+-++.++|.-+|+.||.|..|.|++|.. |.+
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgds  280 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDS  280 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccch
Confidence            456799999999999999999999999999999999987 643

>KOG0123|consensus

Probab=98.03  E-value=1.1e-05  Score=47.91  Aligned_cols=45  Identities=31%  Similarity=0.564  Sum_probs=41.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....+|||.|++..++.+.|++.|+.||+|..++++.+..|+++|
T Consensus       268 ~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG  312 (369)
T KOG0123|consen  268 LQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKG  312 (369)
T ss_pred             ccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccc
Confidence            356789999999999999999999999999999999998888887

>KOG0132|consensus

Probab=97.96  E-value=9.4e-06  Score=51.68  Aligned_cols=37  Identities=27%  Similarity=0.570  Sum_probs=33.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +++||||.|+..+++.+|..+|+.||.|.++.++-.+
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R  457 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR  457 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC
Confidence            5689999999999999999999999999998765443

>KOG4212|consensus

Probab=97.93  E-value=1e-05  Score=49.10  Aligned_cols=42  Identities=17%  Similarity=0.254  Sum_probs=36.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..++|||.|||+++||..|++-|..||.|..+.|+.  .|+++|
T Consensus       535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadime--~GkskG  576 (608)
T KOG4212|consen  535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME--NGKSKG  576 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhc--cCCccc
Confidence            578899999999999999999999999999888832  266665

>KOG4454|consensus

Probab=97.92  E-value=4.2e-06  Score=46.80  Aligned_cols=47  Identities=19%  Similarity=0.306  Sum_probs=40.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCC
Q psy10283         11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK   57 (59)
Q Consensus        11 ~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~r   57 (59)
                      ++.+..++|||+|+...++++.|.++|-+.|+|.++.|..+++++.|
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k   50 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK   50 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc
Confidence            34457889999999999999999999999999999999888775543

>KOG0130|consensus

Probab=97.87  E-value=2.1e-05  Score=41.28  Aligned_cols=41  Identities=24%  Similarity=0.417  Sum_probs=37.5

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      -|||.++....+++++.+.|..||+|..+.+-.|+. |-.||
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KG  115 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKG  115 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccc
Confidence            589999999999999999999999999999999887 76665

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

Probab=97.87  E-value=4.1e-05  Score=46.25  Aligned_cols=26  Identities=23%  Similarity=0.474  Sum_probs=23.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPF   40 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~   40 (59)
                      ..++|||||||+.+++++|.++|..+
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~  199 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDL  199 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHH
Confidence            46789999999999999999999864

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

>KOG0151|consensus

Probab=97.78  E-value=3.8e-05  Score=48.78  Aligned_cols=39  Identities=21%  Similarity=0.421  Sum_probs=35.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ..+++|++||++.+++..|...|..||++..++++..+.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRt  211 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRT  211 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccc
Confidence            567999999999999999999999999999999987653

>KOG4209|consensus

Probab=97.73  E-value=3.2e-05  Score=43.40  Aligned_cols=44  Identities=23%  Similarity=0.254  Sum_probs=40.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....+|+||+.+.++.++++..|+.||.+..+.+..|.. |++||
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~  144 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKG  144 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcce
Confidence            567899999999999999999999999999999999988 77776

>KOG0116|consensus

Probab=97.72  E-value=4.1e-05  Score=46.16  Aligned_cols=35  Identities=23%  Similarity=0.437  Sum_probs=31.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      ...|||+|||++++.+.|+++|..||.|.+..|..
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~v  322 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQV  322 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEE
Confidence            34599999999999999999999999999987754

>KOG0153|consensus

Probab=97.72  E-value=9.1e-05  Score=43.71  Aligned_cols=38  Identities=29%  Similarity=0.505  Sum_probs=33.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .-.+||||+|...+++.++++.|.+||+|..+.++..+
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~  264 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK  264 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc
Confidence            45689999999999999999999999999999877553

>KOG0110|consensus

Probab=97.58  E-value=6.5e-05  Score=47.46  Aligned_cols=43  Identities=23%  Similarity=0.478  Sum_probs=37.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+|.|.|+|+..+-.+++.+|..||.+.+++++.-.. +.+||
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rG  656 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRG  656 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhcc
Confidence            45899999999999999999999999999999987744 55555

>KOG4661|consensus

Probab=97.58  E-value=7.2e-05  Score=46.93  Aligned_cols=39  Identities=21%  Similarity=0.468  Sum_probs=35.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      -.++|||.+|...+...+|+.+|++||+|.-++|+.+..
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaR  442 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNAR  442 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCC
Confidence            467899999999999999999999999999999998753

>KOG0147|consensus

Probab=97.38  E-value=2.7e-05  Score=47.85  Aligned_cols=45  Identities=16%  Similarity=0.373  Sum_probs=41.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      ..+++|+-.++...+..+|.++|+.+|+|.+++++.|+. ++++||
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi  223 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGI  223 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcce
Confidence            356788888999999999999999999999999999998 999986

>KOG0106|consensus

Probab=97.19  E-value=0.00037  Score=38.90  Aligned_cols=32  Identities=25%  Similarity=0.641  Sum_probs=29.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      .++|||+||..+.+.+++.+|..||.+.++.+
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            47999999999999999999999999998764

>KOG4660|consensus

Probab=97.17  E-value=0.00041  Score=42.96  Aligned_cols=34  Identities=26%  Similarity=0.412  Sum_probs=31.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ..+.|+|-|||..+++++|..+|+.||+|.+++-
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~  107 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE  107 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc
Confidence            5678999999999999999999999999998653

>KOG0226|consensus

Probab=97.12  E-value=0.00054  Score=39.20  Aligned_cols=45  Identities=27%  Similarity=0.519  Sum_probs=41.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+.+||+|.|..+++.+.|...|.+|-.-...++++|+. |+++|
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkg  233 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKG  233 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhcccccccccccccc
Confidence            3578999999999999999999999999999999999988 99987

>KOG0129|consensus

Probab=97.12  E-value=0.002  Score=39.77  Aligned_cols=47  Identities=23%  Similarity=0.466  Sum_probs=39.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhc-cCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFA-PFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~-~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +....++||||.||..++.++|-.+|+ .||.|+-+-|=.|++ +=++|
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkG  414 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKG  414 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCC
Confidence            344678999999999999999999998 799999988888865 54444

>KOG3152|consensus

Probab=97.09  E-value=0.00086  Score=38.35  Aligned_cols=35  Identities=9%  Similarity=0.271  Sum_probs=31.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .-+|++++|+.+....|+++|+.||.|-++.+-..
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE  109 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPE  109 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecch
Confidence            45999999999999999999999999999887544

>KOG4208|consensus

Probab=97.01  E-value=0.0017  Score=36.07  Aligned_cols=43  Identities=21%  Similarity=0.402  Sum_probs=37.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccC-CCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPF-GTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~-G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..-+|+..+|+.+.+..+...|.+| |.+.++++.+++. |.|||
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKg   93 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKG   93 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCc
Confidence            3458899999999999999999887 8888888889988 99987

>KOG0115|consensus

Probab=96.86  E-value=0.0013  Score=37.60  Aligned_cols=39  Identities=26%  Similarity=0.394  Sum_probs=34.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT   55 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~   55 (59)
                      ..|||.||+..++.+.+...|+.||.|....+..|..++
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            579999999999999999999999999998887776544

>KOG4210|consensus

Probab=96.85  E-value=0.0016  Score=37.70  Aligned_cols=43  Identities=28%  Similarity=0.472  Sum_probs=37.7

Q ss_pred             CCeEE-EcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLF-VGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~-v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++| ++++++.++.++|+..|..+|.|..+++..++. |.++|
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg  228 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKG  228 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhh
Confidence            44566 999999999999999999999999999998887 77765

>KOG0128|consensus

Probab=96.84  E-value=0.00077  Score=43.63  Aligned_cols=44  Identities=9%  Similarity=0.191  Sum_probs=40.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER   59 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG~   59 (59)
                      ...++|.|.|+..|.+.++.+++.+|.+.+.+++..++|+++|+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~  779 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGK  779 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccc
Confidence            45799999999999999999999999999999998888999885

>KOG0129|consensus

Probab=96.74  E-value=0.0017  Score=40.12  Aligned_cols=34  Identities=26%  Similarity=0.454  Sum_probs=29.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ..++||||.||..++|+.+...|..||.+. +.+.
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP  291 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWP  291 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceE-eecC
Confidence            467899999999999999999999999854 3444

>KOG0120|consensus

Probab=96.65  E-value=0.0025  Score=39.42  Aligned_cols=44  Identities=32%  Similarity=0.579  Sum_probs=40.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|+++||...++..+.++.+.||.+....++.|.. |.++|
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg  332 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKG  332 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccc
Confidence            567899999999999999999999999999999999988 88776

>smart00361 RRM_1 RNA recognition motif

Probab=96.62  E-value=0.0038  Score=28.69  Aligned_cols=29  Identities=14%  Similarity=0.362  Sum_probs=22.2

Q ss_pred             HHHHHHhhc----cCCCeEEEE-EEeCCC---CCCCC
Q psy10283         30 EDDVRKIFA----PFGTIEECT-VLKGPD---GTSKE   58 (59)
Q Consensus        30 ~~~l~~~F~----~~G~i~~~~-v~~d~~---g~~rG   58 (59)
                      +++|+++|+    .||.|.++. ++.++.   |++||
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG   38 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRG   38 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcE
Confidence            567888888    999999995 666653   66666

>KOG4849|consensus

Probab=96.62  E-value=0.00055  Score=40.89  Aligned_cols=42  Identities=21%  Similarity=0.290  Sum_probs=33.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCC--CeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G--~i~~~~v~~d~~-g~~rG   58 (59)
                      -.+|||||-+.+|+++|.+.....|  .+.+++...++. |++||
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG  125 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKG  125 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccc
Confidence            3589999999999999988877665  466666666666 88887

>KOG1457|consensus

Probab=96.44  E-value=0.0026  Score=36.09  Aligned_cols=31  Identities=16%  Similarity=0.430  Sum_probs=26.9

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ++||.||..+++|++|+.+|+.|.-...++|
T Consensus       212 tlfianl~~~~~ed~l~~~~~~~~gf~~l~~  242 (284)
T KOG1457|consen  212 TLFIANLGPNCTEDELKQLLSRYPGFHILKI  242 (284)
T ss_pred             hHhhhccCCCCCHHHHHHHHHhCCCceEEEE
Confidence            6999999999999999999999966555553

>PF13893 RRM_5: RNA recognition motif

Probab=96.37  E-value=0.0056  Score=26.73  Aligned_cols=20  Identities=25%  Similarity=0.635  Sum_probs=15.9

Q ss_pred             HHHhhccCCCeEEEEEEeCC
Q psy10283         33 VRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        33 l~~~F~~~G~i~~~~v~~d~   52 (59)
                      |.++|++||.|.++.+..+.
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            57899999999999886654

(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 ....

>KOG4211|consensus

Probab=96.24  E-value=0.023  Score=35.22  Aligned_cols=43  Identities=16%  Similarity=0.251  Sum_probs=32.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....-|-+..||+++|++++.++|+.++ |+.+.+.++. |+..|
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~-Gr~sG   50 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRN-GRPSG   50 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccC-CCcCc
Confidence            3445567789999999999999999986 7776555542 55544

>KOG1190|consensus

Probab=96.16  E-value=0.011  Score=36.06  Aligned_cols=37  Identities=27%  Similarity=0.489  Sum_probs=32.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..+-+.++|||.+++|+++-+++.+||+|..+...+.
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG   63 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG   63 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeecc
Confidence            4567899999999999999999999999999876543

>KOG0110|consensus

Probab=96.16  E-value=0.0069  Score=38.78  Aligned_cols=37  Identities=30%  Similarity=0.434  Sum_probs=33.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ++||+.||++.++.+++...|...|.|.++.|.+.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd  552 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKD  552 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEecccc
Confidence            3499999999999999999999999999998877665

>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=95.30  E-value=0.03  Score=27.99  Aligned_cols=33  Identities=18%  Similarity=0.389  Sum_probs=20.2

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      -|.+.+++..++.++|++.|+.||.|.-+.+..
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~   35 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR   35 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--T
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecC
Confidence            467777999999999999999999888776544

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

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

Probab=95.23  E-value=0.043  Score=26.67  Aligned_cols=29  Identities=28%  Similarity=0.587  Sum_probs=19.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEE
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEE   45 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~   45 (59)
                      ..-.+++ .|......+|.++|++||.|.-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~V   37 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYV   37 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEE
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEE
Confidence            3344454 8899999999999999999763

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG1855|consensus

Probab=95.00  E-value=0.047  Score=33.54  Aligned_cols=37  Identities=22%  Similarity=0.454  Sum_probs=33.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..+.|-+-|||.+-.-+.|.++|+.+|.|..++|...
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckP  266 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKP  266 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCC
Confidence            5678889999999888999999999999999998766

>KOG1457|consensus

Probab=94.97  E-value=0.11  Score=29.76  Aligned_cols=34  Identities=21%  Similarity=0.358  Sum_probs=27.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ..++|||.+||.++...+|..+|..|---+.+.+
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslL   66 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLL   66 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceee
Confidence            4789999999999999999999998844444433

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

Probab=94.63  E-value=0.063  Score=23.61  Aligned_cols=32  Identities=28%  Similarity=0.318  Sum_probs=22.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      +.|-|.+.+....+ .+...|.+||+|.+..+.
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~   33 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP   33 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC
Confidence            34566666655554 455688899999998765

>KOG4211|consensus

Probab=94.60  E-value=0.095  Score=32.66  Aligned_cols=43  Identities=16%  Similarity=0.208  Sum_probs=32.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEE-EEEEeCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEE-CTVLKGPDGTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~-~~v~~d~~g~~rG   58 (59)
                      ..-|-+..||+.++++++.++|+-.--+.. +-++.|+.|++-|
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tG  146 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTG  146 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCccc
Confidence            445777999999999999999998765555 4456666566543

>KOG1995|consensus

Probab=94.32  E-value=0.057  Score=32.28  Aligned_cols=44  Identities=20%  Similarity=0.345  Sum_probs=34.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEE--------EEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~--------~~v~~d~~-g~~rG   58 (59)
                      ...++||-.|+..+++..+.++|.++|.|..        +.+-+|++ +++||
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KG  117 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKG  117 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCC
Confidence            5668999999999999999999999997754        44455555 55554

>KOG0112|consensus

Probab=93.69  E-value=0.022  Score=37.57  Aligned_cols=37  Identities=27%  Similarity=0.527  Sum_probs=32.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..++||+|||+..+++.+++..|..+|.+.++.+-..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP  407 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTP  407 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccC
Confidence            4568999999999999999999999999999876543

>KOG0105|consensus

Probab=93.64  E-value=0.19  Score=28.08  Aligned_cols=38  Identities=13%  Similarity=0.163  Sum_probs=33.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ...++-|..||.+-++++|++..-..|.++-..+.+|-
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg  151 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDG  151 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeeccc
Confidence            34579999999999999999999999999888877663

>KOG4206|consensus

Probab=93.49  E-value=0.21  Score=28.21  Aligned_cols=38  Identities=18%  Similarity=0.479  Sum_probs=32.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      +...-+|+.|||..++.+.+..+|.+|....+++++..
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~  181 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP  181 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC
Confidence            35667999999999999999999999988888776553

>KOG4676|consensus

Probab=93.47  E-value=0.061  Score=32.83  Aligned_cols=35  Identities=20%  Similarity=0.374  Sum_probs=31.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .-|.|.||.+..+.++++.+|...|+|.+++++-+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~   42 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPN   42 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCC
Confidence            36889999999999999999999999999887654

>KOG1190|consensus

Probab=93.19  E-value=0.23  Score=30.61  Aligned_cols=38  Identities=18%  Similarity=0.371  Sum_probs=32.0

Q ss_pred             CCeEEEcCCC-CCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         16 DKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        16 ~~~l~v~~L~-~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ..-|.|.||. ..+|.+.|.-+|+.||.|.+++|+.++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk  335 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK  335 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC
Confidence            4667888886 4579999999999999999999988753

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=93.15  E-value=0.38  Score=23.86  Aligned_cols=42  Identities=5%  Similarity=0.040  Sum_probs=32.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhcc--CCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAP--FGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~--~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++|-+.|+|...+.+.|.+++..  .|...=+.++.|.. +.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~G   46 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLG   46 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceE
Confidence            47889999999999999888754  36677778888876 44444

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0128|consensus

Probab=91.36  E-value=0.0071  Score=39.43  Aligned_cols=43  Identities=30%  Similarity=0.482  Sum_probs=35.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      .++|+.||+..+.+.++...|+.+|.+..+++..... ++.||+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~  711 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGK  711 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccc
Confidence            3689999999999999999999999998887764444 666663

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=91.30  E-value=0.47  Score=23.22  Aligned_cols=29  Identities=17%  Similarity=0.360  Sum_probs=18.0

Q ss_pred             eEEEcCCCCCCcHHH----HHHhhccCC-CeEEE
Q psy10283         18 KLFVGMLSKQQNEDD----VRKIFAPFG-TIEEC   46 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~----l~~~F~~~G-~i~~~   46 (59)
                      -|||.|||...+...    |+.++..+| +|..+
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v   37 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV   37 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE
Confidence            589999999887654    667777884 66654

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF15513 DUF4651: Domain of unknown function (DUF4651)

Probab=90.86  E-value=0.4  Score=21.98  Aligned_cols=18  Identities=28%  Similarity=0.578  Sum_probs=15.6

Q ss_pred             HHHHHhhccCCCeEEEEE
Q psy10283         31 DDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        31 ~~l~~~F~~~G~i~~~~v   48 (59)
                      .++++.|+.+|.|.-+.+
T Consensus         9 ~~iR~~fs~lG~I~vLYv   26 (62)
T PF15513_consen    9 AEIRQFFSQLGEIAVLYV   26 (62)
T ss_pred             HHHHHHHHhcCcEEEEEE
Confidence            578999999999998765

>KOG0112|consensus

Probab=88.54  E-value=1  Score=30.36  Aligned_cols=35  Identities=23%  Similarity=0.323  Sum_probs=30.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ...+++|+++|...+....|...|..||.|..+.+
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy  487 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY  487 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeec
Confidence            35678999999999999999999999999988653

>KOG0106|consensus

Probab=87.42  E-value=0.59  Score=26.39  Aligned_cols=32  Identities=25%  Similarity=0.342  Sum_probs=28.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC   46 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~   46 (59)
                      ..+.+.+-+++..+.+.+|.+.|.++|.+...
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~  129 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYV  129 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchh
Confidence            46778899999999999999999999998443

>KOG4454|consensus

Probab=86.51  E-value=0.19  Score=28.68  Aligned_cols=42  Identities=24%  Similarity=0.442  Sum_probs=35.3

Q ss_pred             CCeEEEcC----CCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCC
Q psy10283         16 DKKLFVGM----LSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK   57 (59)
Q Consensus        16 ~~~l~v~~----L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~r   57 (59)
                      ..+++.|+    |...++++.+...|+..|.+...++..+.+|+.+
T Consensus        80 q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnr  125 (267)
T KOG4454|consen   80 QRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNR  125 (267)
T ss_pred             hcccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCcc
Confidence            45677888    8888999999999999999999999888775544

>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]

Probab=84.97  E-value=2  Score=24.95  Aligned_cols=35  Identities=11%  Similarity=0.013  Sum_probs=27.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ....|+|||+.++..-+..+++..-.+.+..+|..
T Consensus        96 ~~~vVaNlPY~Isspii~kll~~~~~~~~~v~M~Q  130 (259)
T COG0030          96 PYKVVANLPYNISSPILFKLLEEKFIIQDMVLMVQ  130 (259)
T ss_pred             CCEEEEcCCCcccHHHHHHHHhccCccceEEEEeH
Confidence            35668999999999999998887666656666544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=84.85  E-value=1.1  Score=27.37  Aligned_cols=34  Identities=18%  Similarity=0.416  Sum_probs=25.5

Q ss_pred             CeEEEcCCCCCCcHHH----H--HHhhccCCCeEEEEEEe
Q psy10283         17 KKLFVGMLSKQQNEDD----V--RKIFAPFGTIEECTVLK   50 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~----l--~~~F~~~G~i~~~~v~~   50 (59)
                      .-+||-+|++.+-.++    |  .+.|.+||.|.++.|-+
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNk  154 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNK  154 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecc
Confidence            3489989988875543    3  36899999999886643

>KOG1456|consensus

Probab=84.59  E-value=2.8  Score=25.94  Aligned_cols=40  Identities=25%  Similarity=0.429  Sum_probs=32.9

Q ss_pred             CCCeEEEcCCCCCC-cHHHHHHhhccCCCeEEEEEEeCCCC
Q psy10283         15 PDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKGPDG   54 (59)
Q Consensus        15 ~~~~l~v~~L~~~~-~~~~l~~~F~~~G~i~~~~v~~d~~g   54 (59)
                      .++-+-|.+|.... .-+.|..+|..||.|++++.|+.+.|
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~g  326 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPG  326 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccc
Confidence            45678888998766 44778999999999999999987654

>KOG2891|consensus

Probab=83.51  E-value=1.5  Score=26.16  Aligned_cols=36  Identities=22%  Similarity=0.431  Sum_probs=27.5

Q ss_pred             CCCCeEEEcCCCCC------------CcHHHHHHhhccCCCeEEEEEE
Q psy10283         14 PPDKKLFVGMLSKQ------------QNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        14 ~~~~~l~v~~L~~~------------~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ....++|..++|..            -+++.|+..|+.||.|..+.|+
T Consensus       147 erpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdip  194 (445)
T KOG2891|consen  147 ERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIP  194 (445)
T ss_pred             CCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCc
Confidence            34557777777643            3567799999999999998875

>KOG2314|consensus

Probab=81.77  E-value=0.96  Score=29.16  Aligned_cols=45  Identities=18%  Similarity=0.148  Sum_probs=33.1

Q ss_pred             CCCCeEEEcCCCCCCcH--H----HHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNE--D----DVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~--~----~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....-++|.|+|---..  +    -|.++|+++|++.....+.+.+|..+|
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG  106 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKG  106 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeee
Confidence            34556888888754322  2    255689999999999999888866777

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=80.23  E-value=1.8  Score=25.74  Aligned_cols=38  Identities=18%  Similarity=0.311  Sum_probs=32.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..+.|...|+...++-..+-.-|.+||+|+++.++.+.
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~   51 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSN   51 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCC
Confidence            34567788999888888888999999999999998776

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	59
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		8e-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		2e-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 = 75.5 bits (184), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 39/42 (92%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          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 = 2e-10,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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 = 60.5 bits (145), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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	59
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-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	4e-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	2e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-09
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-04
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-05
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-07
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-07
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-07
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-07
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-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
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-05
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-05
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	9e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-04
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-04
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-04
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	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
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	7e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	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 = 74.2 bits (183), Expect = 9e-20
 Identities = 30/44 (68%), Positives = 39/44 (88%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            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 = 74.2 bits (183), Expect = 4e-19
 Identities = 24/42 (57%), Positives = 35/42 (83%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           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 = 51.8 bits (125), Expect = 2e-10
 Identities = 12/37 (32%), Positives = 22/37 (59%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
          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 = 62.3 bits (152), Expect = 4e-15
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 8  WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           +        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 = 54.1 bits (131), Expect = 2e-11
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
             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 = 41.0 bits (97), Expect = 2e-06
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          +  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 = 52.7 bits (127), Expect = 3e-11
 Identities = 12/46 (26%), Positives = 23/46 (50%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
              K+ V  +  Q N+ ++R++F+ FG ++   + K   GT   R
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58

>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 = 53.0 bits (128), Expect = 6e-11
 Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 18  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
            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 = 41.0 bits (97), Expect = 2e-06
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
           L V  L +   +++ R +F   G IE C +++
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR 36

>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 = 49.2 bits (118), Expect = 6e-10
 Identities = 11/39 (28%), Positives = 18/39 (46%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
           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 = 49.2 bits (118), Expect = 8e-10
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
              KLF+G L+++ NE  ++ +F   G I E  ++K     S+
Sbjct: 5  DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR 48

>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 = 48.4 bits (116), Expect = 8e-10
 Identities = 11/40 (27%), Positives = 18/40 (45%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
                KL VG +S      ++R  F  +G + EC ++K 
Sbjct: 6  SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45

>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 = 50.5 bits (121), Expect = 1e-09
 Identities = 10/44 (22%), Positives = 19/44 (43%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
                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 = 41.6 bits (98), Expect = 2e-06
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          +LFVG L     E+D +++F  +G   E  + +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINR 56

>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 = 48.0 bits (115), Expect = 1e-09
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
           K+FVG +S      ++R +F   G + EC V+K 
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44

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

 Score = 48.5 bits (116), Expect = 1e-09
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           P K++    L+    E  ++ +   +G +EE  +L  P      
Sbjct: 4  IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL 48

>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 = 47.6 bits (114), Expect = 2e-09
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
              +LFVG L     E+++RK+F  +G   E  + K 
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD 50

>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 = 47.7 bits (114), Expect = 2e-09
 Identities = 9/46 (19%), Positives = 20/46 (43%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
                 +FV  L  +     ++++F+  G +    +L+  DG S+
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR 56

>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 = 46.9 bits (112), Expect = 3e-09
 Identities = 13/38 (34%), Positives = 17/38 (44%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
               L+VG L     E D+R  F  FG I   TV++ 
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR 47

>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 = 47.8 bits (114), Expect = 3e-09
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           +    KL V  L    ++ D++++FA FGT+++  V     G S 
Sbjct: 31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 76

>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 = 47.3 bits (113), Expect = 4e-09
 Identities = 13/47 (27%), Positives = 23/47 (48%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            +    KL V  L    ++ D++++FA FGT+++  V     G S 
Sbjct: 24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL 70

>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 = 46.9 bits (112), Expect = 4e-09
 Identities = 12/44 (27%), Positives = 23/44 (52%)

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

>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 = 47.2 bits (113), Expect = 4e-09
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           L++  L    +E ++  +  PFG +    +L+   GTS+
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 66

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

 Score = 46.9 bits (112), Expect = 4e-09
 Identities = 12/38 (31%), Positives = 20/38 (52%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
            + +LFV        E ++ +IF PFG ++E  +L G
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 66

>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 = 46.4 bits (111), Expect = 5e-09
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
           KLF+G L ++  E ++R +F  +G + EC ++K 
Sbjct: 9  VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN 43

>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 = 46.4 bits (111), Expect = 5e-09
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          P    ++V  L      +D+ +IF+ +G + + T++K  D   SK
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK 58

>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 = 46.4 bits (111), Expect = 5e-09
 Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               L+VG L     ED +R IF PFG I+   ++K  D G SK
Sbjct: 3  SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK 47

>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 = 46.4 bits (111), Expect = 5e-09
 Identities = 8/46 (17%), Positives = 20/46 (43%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
              K+ +G L++   +D + +IF+ +G I+   +          +
Sbjct: 2  MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSK 47

>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 = 48.0 bits (115), Expect = 5e-09
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 12  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           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 = 37.2 bits (87), Expect = 4e-05
 Identities = 8/39 (20%), Positives = 15/39 (38%)

Query: 13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          L   ++L+VG +     E+ +   F     +   T   G
Sbjct: 1  LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39

>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 = 46.5 bits (111), Expect = 6e-09
 Identities = 13/35 (37%), Positives = 18/35 (51%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          K LFV  L+    E+ + K F+ FG +E    LK 
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46

>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 = 46.5 bits (111), Expect = 6e-09
 Identities = 10/42 (23%), Positives = 20/42 (47%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
           LF+  L+    E+ ++ +F+  G I+ CT+ K  +      
Sbjct: 7  GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL 48

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

 Score = 47.9 bits (114), Expect = 6e-09
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 12  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            +    KL V  L    ++ D++++FA FGT+++  V     G S 
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 129

>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 = 46.0 bits (110), Expect = 7e-09
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           P+  L V  LS    E D+R++F+ +G I + +++       S+
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 57

>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 = 47.7 bits (114), Expect = 8e-09
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               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 = 34.6 bits (80), Expect = 5e-04
 Identities = 7/35 (20%), Positives = 14/35 (40%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          ++L+VG +     E+ +   F     +   T   G
Sbjct: 5  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39

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

 Score = 45.7 bits (109), Expect = 1e-08
 Identities = 9/44 (20%), Positives = 20/44 (45%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
              KLF+  L     ++++ +I    GT+++  ++    G  K
Sbjct: 15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK 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 = 47.7 bits (114), Expect = 1e-08
 Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               +++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 = 41.5 bits (98), Expect = 1e-06
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           L    +++VG +  +  ED +R+ FAPFG I+   +         K
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70

>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 = 45.7 bits (109), Expect = 1e-08
 Identities = 7/44 (15%), Positives = 19/44 (43%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
               LF+G L+  ++  +++   +      +  V+    GT++
Sbjct: 15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNR 58

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

 Score = 45.7 bits (109), Expect = 1e-08
 Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 11 TPLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
            +PP  +LF+G L  +  +++D+ +IF+P+G I +  +   
Sbjct: 5  HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 46

>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 = 45.8 bits (109), Expect = 1e-08
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 12 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
          P   + ++F+G L+     + DV  IF+ +G +  C+V KG
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG 63

>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 = 45.7 bits (109), Expect = 1e-08
 Identities = 12/41 (29%), Positives = 24/41 (58%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            +FVG +  + +E ++R  FA +G+++E  ++    G SK
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSK 50

>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 = 45.3 bits (108), Expect = 2e-08
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
            + KLFVG LS   NE  + ++F+ +G I E  V+K
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK 46

>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 = 45.2 bits (107), Expect = 2e-08
 Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVLKGPDGTSKER 59
            + +LF+G + K +  +++ +  A     + +  V        K R
Sbjct: 6  SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNR 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 = 44.9 bits (107), Expect = 2e-08
 Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          P + +++G +   Q E+ +  + +  G +    ++  P  G SK
Sbjct: 1  PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSK 44

>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 = 44.4 bits (106), Expect = 3e-08
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
             + L+VG L+++ ++  +   F PFG I +  +    +    +
Sbjct: 5  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 49

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

 Score = 45.5 bits (108), Expect = 3e-08
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
              + L+VG L+++ ++  +   F PFG I +  +    +    +
Sbjct: 61  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

>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 = 44.2 bits (105), Expect = 4e-08
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
           KL++G LS     DD+R++F          VL 
Sbjct: 9  NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 42

>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 = 44.1 bits (105), Expect = 5e-08
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
              +LFV  LS   +E+D+ K+F+ +G + E            K
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK 50

>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 = 44.7 bits (106), Expect = 5e-08
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           P+  L V  LS    E D+R++F+ +G I + +++       S+
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 44.2 bits (105), Expect = 5e-08
 Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 12 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
                +LF+G L  +  +++D+ +IF+P+G I +  +   
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 58

>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 = 45.3 bits (108), Expect = 6e-08
 Identities = 7/44 (15%), Positives = 19/44 (43%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
               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 = 38.4 bits (90), Expect = 2e-05
 Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 12  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            +   + L    LS    ED+++++F     I   +     DG SK
Sbjct: 95  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSK 136

>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 = 44.2 bits (105), Expect = 6e-08
 Identities = 11/40 (27%), Positives = 20/40 (50%)

Query: 9  NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
          +  P  P+K L++  LS +  E D+  +FA F   +   +
Sbjct: 18 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI 57

>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 = 44.9 bits (106), Expect = 6e-08
 Identities = 12/43 (27%), Positives = 21/43 (48%)

Query: 12  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
             P D K++VG L    N+ ++ + F  +G +    V + P G
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG 111

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

 Score = 44.0 bits (104), Expect = 7e-08
 Identities = 4/42 (9%), Positives = 15/42 (35%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          ++ +++         DD+++     G +    + +      K
Sbjct: 11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK 52

>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 = 43.4 bits (103), Expect = 8e-08
 Identities = 9/34 (26%), Positives = 19/34 (55%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
            +FVG  +    ED++R+ F+ +G + +  + K
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK 39

>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 = 43.4 bits (103), Expect = 8e-08
 Identities = 9/37 (24%), Positives = 19/37 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
             + L+VG L+++ ++  +   F PFG I +  +  
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 46

>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 = 8e-08
 Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK-GPDGTSK 57
           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 = 43.8 bits (104), Expect = 3e-07
 Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)

Query: 17  KKLFVGMLSKQQNEDD-VRKIFAPFGTIEECTVLKGPDGTSK 57
           + L V  L    N+ D + +  +   +   C +  G DG  K
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLK 226

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

 Score = 43.7 bits (103), Expect = 9e-08
 Identities = 10/38 (26%), Positives = 17/38 (44%)

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

>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 = 43.3 bits (103), Expect = 1e-07
 Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
            K+FVG +     E ++R+ F  FG + E  ++   +   + R
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE-KQRPR 52

>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 = 43.4 bits (103), Expect = 1e-07
 Identities = 14/37 (37%), Positives = 18/37 (48%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
           K+FVG L     +  +RK F  FG IEE  V+    
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ 54

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

 Score = 43.2 bits (102), Expect = 1e-07
 Identities = 8/38 (21%), Positives = 13/38 (34%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
          P    + +  L     E D+ +    FG I    V+  
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

>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 = 42.6 bits (101), Expect = 1e-07
 Identities = 7/35 (20%), Positives = 19/35 (54%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
            K+FVG  ++    +++++ F  +G + +  + K
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK 45

>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 = 43.1 bits (102), Expect = 1e-07
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               +FVG LS +   +D++  FAPFG I +  V+K    G SK
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSK 57

>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 = 43.0 bits (102), Expect = 1e-07
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
            +  + V  LS+   E D++++F PFG+I    + K    G SK
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK 57

>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 = 43.0 bits (102), Expect = 1e-07
 Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             K+L V  +  +  + D+R++F  FG I +  ++      SK
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSK 55

>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 = 43.0 bits (102), Expect = 1e-07
 Identities = 12/38 (31%), Positives = 23/38 (60%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
           +KLF+G LS +  E+ +R  +  +G + +C V++ P 
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 64

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 42.6 bits (101), Expect = 2e-07
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
            K+FVG LS   ++ D++  F  FG + +CT+   P+ T + R
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPN-TGRSR 53

>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 = 44.2 bits (105), Expect = 2e-07
 Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           +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 = 44.2 bits (105), Expect = 2e-07
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
              KK+FVG + +   E  +R  F  +G IE   ++     + K+R
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG-SGKKR 146

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

 Score = 42.6 bits (101), Expect = 2e-07
 Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 1/44 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
              ++FV  L        ++  F   G +    +    +G SK
Sbjct: 6  SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSK 48

>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 = 42.7 bits (101), Expect = 2e-07
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
              +L+VG L     ED +R IF PFG IE   ++   + G SK
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68

>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 = 43.7 bits (104), Expect = 2e-07
 Identities = 9/40 (22%), Positives = 18/40 (45%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
               K+FVG +       +  + F+ +GTI +  ++   D
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124

>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 = 43.7 bits (104), Expect = 2e-07
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
            K+F+G L+    ED++R+ F  +GT+ +  ++K P  G S+
Sbjct: 3  SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSR 45

>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 = 43.6 bits (103), Expect = 2e-07
 Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           L     L+VG LS    E+ + ++F+  G I++  +       T+ 
Sbjct: 35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC 81

>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 = 42.1 bits (100), Expect = 2e-07
 Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               L++  L     + D+ K+  P+G I     +        K
Sbjct: 3  SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK 47

>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 = 42.7 bits (101), Expect = 3e-07
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          P    LF+  L ++  + D+ ++F PFG +    V        SK
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

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

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 3/50 (6%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGT--IEECTVLKGPD-GTSK 57
                  + +  ++     D +    +P+ +  +    ++K      ++
Sbjct: 4  HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNR 53

>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 = 42.2 bits (100), Expect = 3e-07
 Identities = 11/38 (28%), Positives = 20/38 (52%)

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

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

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             K+L V  +  +  + D+R++F  FG I +  ++    G SK
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SK 69

>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 = 42.2 bits (100), Expect = 3e-07
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
            K+F+G LS Q  ++ +R+ F  FG ++EC V++ P 
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

>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 = 42.3 bits (100), Expect = 3e-07
 Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
            K +F+  LS    E+ + ++   FG ++   V+  PD   SK
Sbjct: 14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK 57

>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 = 42.1 bits (99), Expect = 3e-07
 Identities = 11/38 (28%), Positives = 18/38 (47%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
           P + L +  L  +  E +V  +  PFG +    +LKG
Sbjct: 13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG 50

>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 = 41.8 bits (99), Expect = 3e-07
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          PL     +FVG LS +     +   FAPFG I +  V+K    G SK
Sbjct: 2  PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSK 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 = 42.8 bits (101), Expect = 3e-07
 Identities = 8/37 (21%), Positives = 17/37 (45%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
             + L V  +    +E  +R++F  +G IE   ++ 
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC 76

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

 Score = 41.3 bits (98), Expect = 4e-07
 Identities = 14/36 (38%), Positives = 24/36 (66%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
          K+F+G LS Q  ++ +R+ F  FG ++EC V++ P 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 37

>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 = 42.2 bits (99), Expect = 4e-07
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
           P + + +  L     E +V  +  PFG +    +LKG
Sbjct: 29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66

>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 = 41.9 bits (99), Expect = 4e-07
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
             K L +  LS    E+ ++++F     I+   V +  +G SK
Sbjct: 13 GESKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSK 53

>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 = 41.3 bits (98), Expect = 4e-07
 Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           LFVG L+   +++ +R  F  F +     V+     G+S+
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 43

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 41.5 bits (98), Expect = 4e-07
 Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 7/44 (15%)

Query: 8  WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
             T        ++G +     E D+  +F  FG I +      
Sbjct: 26 RVTT-------AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE 62

>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 = 40.9 bits (97), Expect = 5e-07
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          K+FVG LS    E+ +R+ F  FG +E   +      T+K R
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK-TNKRR 41

>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 = 41.7 bits (98), Expect = 5e-07
 Identities = 8/41 (19%), Positives = 15/41 (36%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
            +     + V  L +   E D+ +    FGTI    ++  
Sbjct: 10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF 50

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

 Score = 41.6 bits (98), Expect = 6e-07
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
          P    LF+  L ++  + D+   F PFG +    V        SK
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK 82

>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 = 41.5 bits (98), Expect = 6e-07
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 7/44 (15%)

Query: 8  WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
           NCT       ++ G ++    +  +R+ F+PFG I E  V   
Sbjct: 24 KNCT-------VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

>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 = 41.1 bits (97), Expect = 7e-07
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
             L V  L  +  E D+++ F+ FG +    V K   
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK 52

>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 = 41.1 bits (97), Expect = 7e-07
 Identities = 7/36 (19%), Positives = 18/36 (50%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
              L V  L+ + + D +R++F  +G + +  + +
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR 47

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.5 bits (96), Expect = 7e-07
 Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          K+FVG LS     +DV+  F  FG +++  ++     T++ R
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT-TNRHR 41

>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 = 41.2 bits (97), Expect = 8e-07
 Identities = 9/43 (20%), Positives = 17/43 (39%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
              D +++VG L       D+  +F  +G I +  +     G
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG 60

>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 = 40.6 bits (96), Expect = 8e-07
 Identities = 7/34 (20%), Positives = 18/34 (52%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          + ++VG L      + V+++F+ FG +    ++ 
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIY 35

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

 Score = 41.7 bits (98), Expect = 8e-07
 Identities = 7/37 (18%), Positives = 18/37 (48%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
               L V  L+ + + D +R++F  +G + +  + +
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81

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

 Score = 40.7 bits (96), Expect = 9e-07
 Identities = 8/37 (21%), Positives = 19/37 (51%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
          K++VG L     + ++ + F+ +G +    + + P G
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG 38

>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 = 41.9 bits (99), Expect = 1e-06
 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 17  KKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
           +++ +  LS +  +E+ +R+ F  FG+IE+  +  G    S   
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 = 38.8 bits (91), Expect = 2e-05
 Identities = 5/43 (11%), Positives = 14/43 (32%), Gaps = 1/43 (2%)

Query: 16  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
           +  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 = 38.8 bits (91), Expect = 2e-05
 Identities = 10/36 (27%), Positives = 13/36 (36%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
          + V  L K  N++ V K F   G I    V      
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK 79

>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 = 40.3 bits (95), Expect = 1e-06
 Identities = 7/33 (21%), Positives = 14/33 (42%)

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

>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 = 40.3 bits (95), Expect = 2e-06
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           L+V  L    +++ +RK F+PFGTI    V+    G SK
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSK 55

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.0 bits (94), Expect = 2e-06
 Identities = 6/34 (17%), Positives = 14/34 (41%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          + +FV    +  +   + + F  FG +    + K
Sbjct: 9  RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK 42

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 39.9 bits (94), Expect = 2e-06
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               LFV  + ++  E+D+   FA +G I+   +      G  K
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65

>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 = 40.0 bits (94), Expect = 2e-06
 Identities = 8/35 (22%), Positives = 18/35 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
               LFV  + ++  ED++++ F  +G I+   +
Sbjct: 24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHL 58

>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 = 41.4 bits (96), Expect = 2e-06
 Identities = 9/37 (24%), Positives = 17/37 (45%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
              K LFV  ++    E  +R+ F  +G I+   ++ 
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136

>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 = 40.0 bits (94), Expect = 2e-06
 Identities = 10/40 (25%), Positives = 14/40 (35%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
             K L+V  L    +E+ + K F          V K  D
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD 52

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 39.7 bits (93), Expect = 2e-06
 Identities = 5/34 (14%), Positives = 14/34 (41%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          +KL +  +      + +  +   +G +E C  + 
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN 49

>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 = 40.6 bits (95), Expect = 2e-06
 Identities = 7/36 (19%), Positives = 18/36 (50%)

Query: 15  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
               L V  L+ + + D +R++F  +G + +  + +
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104

>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 = 39.5 bits (93), Expect = 3e-06
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECT-VLKGPD-GTSK 57
               +F+G L  + +E  +   F+ FG I +   +++ PD G SK
Sbjct: 3  SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK 48

>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 = 40.0 bits (94), Expect = 3e-06
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               LFV  + ++  E+D+   FA +G I+   +      G  K
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64

>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 = 40.2 bits (94), Expect = 3e-06
 Identities = 11/50 (22%), Positives = 21/50 (42%)

Query: 9  NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          +  P  P+ +++V  L+K   E D++ IF  +      T     D    +
Sbjct: 38 SYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK 87

>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 = 40.6 bits (94), Expect = 4e-06
 Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 52
           P+  +++  L+++  +D+++K    IF+ FG I +  V +  
Sbjct: 7  RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL 49

>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 = 40.2 bits (95), Expect = 4e-06
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 15  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
               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 = 34.8 bits (81), Expect = 4e-04
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          + L+VG L K   ED +++ F   G I    ++   +  + 
Sbjct: 1  RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV 41

>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 = 39.8 bits (93), Expect = 5e-06
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
                LFV  + ++  ED++++ F  +G I+   +      G SK
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 39.2 bits (91), Expect = 5e-06
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          +K+FVG L    +ED++   F  FG +      K    +  
Sbjct: 9  RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYF 49

>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 = 38.8 bits (91), Expect = 6e-06
 Identities = 8/36 (22%), Positives = 18/36 (50%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
           D  ++VG L ++ +E  + ++F   G +    + K
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK 49

>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 = 38.8 bits (91), Expect = 6e-06
 Identities = 9/37 (24%), Positives = 19/37 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
             + L+VG LS+   E  + ++F+  G  + C ++ 
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT 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 = 39.2 bits (92), Expect = 1e-05
 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 19  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
           +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 = 34.9 bits (81), Expect = 4e-04
 Identities = 12/40 (30%), Positives = 17/40 (42%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
           P  P   L+VG L     E  + + F+P G I    V +
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR 49

>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 = 38.2 bits (89), Expect = 1e-05
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          + ++VG +       D+   F+  G+I   T+L 
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70

>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 = 37.5 bits (88), Expect = 1e-05
 Identities = 6/34 (17%), Positives = 16/34 (47%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          + ++VG +      +++   F   G++   T+L 
Sbjct: 7  RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILC 40

>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 = 37.7 bits (88), Expect = 2e-05
 Identities = 7/44 (15%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
            + +F   L+ +    D+   F+  G + +  ++   +   SK
Sbjct: 24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67

>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 = 37.2 bits (87), Expect = 3e-05
 Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 52
           P+  +++  L+++  +D+++K    IF+ FG I +  V +  
Sbjct: 6  RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL 48

>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 = 37.2 bits (87), Expect = 3e-05
 Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            +F+  L K  +   +   F+ FG I  C V+      SK
Sbjct: 6  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSK 45

>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 = 36.9 bits (86), Expect = 4e-05
 Identities = 7/37 (18%), Positives = 18/37 (48%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
             + +FVG +  +  E+ ++ IF+  G +    ++ 
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY 42

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 36.7 bits (84), Expect = 9e-05
 Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 9/47 (19%)

Query: 14  PPDKKLFVGMLS---------KQQNEDDVRKIFAPFGTIEECTVLKG 51
             +K L+VG +            Q E  +R +F+  G I+    ++ 
Sbjct: 132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES 178

>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 = 36.4 bits (84), Expect = 1e-04
 Identities = 8/41 (19%), Positives = 18/41 (43%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
           PP   L +  +    +E+D++ +F+  G + +       D 
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 158

>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 = 35.8 bits (83), Expect = 1e-04
 Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 13 LPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          LPP+  + L++  L  +   +++  IF  +G I +  V       ++
Sbjct: 3  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETR 47

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 35.8 bits (83), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 13/40 (32%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
            +  +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 = 35.6 bits (82), Expect = 1e-04
 Identities = 4/46 (8%), Positives = 17/46 (36%), Gaps = 4/46 (8%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 52
              P + + +  ++ +  ++ ++     + +  G I +  V    
Sbjct: 24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD 69

>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 = 35.3 bits (81), Expect = 1e-04
 Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 2/39 (5%)

Query: 15 PDKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
            + L V  G L    + + +  +    G ++   +   
Sbjct: 24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 62

>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 = 34.6 bits (80), Expect = 2e-04
 Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 9/44 (20%)

Query: 8  WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
             T       L+V           +R  F+PFG I + ++   
Sbjct: 14 KGNT-------LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP 48

>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 = 34.6 bits (80), Expect = 2e-04
 Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
          P    + V  +    + D++   F  +  I     L     G   
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 35.4 bits (81), Expect = 3e-04
 Identities = 8/41 (19%), Positives = 18/41 (43%)

Query: 14  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
           PP   L +  +    +E+D++ +F+  G + +       D 
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 189

>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 = 34.2 bits (79), Expect = 4e-04
 Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          P  P    F+G L     E+ +++ F     I    + + P    + +
Sbjct: 11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 57

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 34.9 bits (80), Expect = 4e-04
 Identities = 4/28 (14%), Positives = 11/28 (39%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIE 44
            ++VG  S    +  + ++    G  +
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYD 83

>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 = 34.0 bits (78), Expect = 4e-04
 Identities = 4/33 (12%), Positives = 13/33 (39%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
             +    L       ++++ F+ FG++    +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL 42

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 33.8 bits (78), Expect = 4e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIF-APFGTIEECTVLKGPDGTSK 57
          P+  LFVG L+   ++  + + F   + +     V+    G SK
Sbjct: 8  PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSK 51

>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 = 34.1 bits (78), Expect = 6e-04
 Identities = 6/48 (12%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
               D  + +  L     ++++ + F+    +     L   P+G   
Sbjct: 37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKIT 84

>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 = 33.3 bits (77), Expect = 7e-04
 Identities = 5/27 (18%), Positives = 13/27 (48%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIE 44
           L++G L+    ++D+ +     G  +
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVND 29

>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 = 33.4 bits (77), Expect = 7e-04
 Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
          P    + V  +    + D++   F  +  I     L     G   
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 33.4 bits (77), Expect = 8e-04
 Identities = 8/31 (25%), Positives = 11/31 (35%)

Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFG 41
           P  P    +VG L     + D+  IF    
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS 40

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	59
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.6
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.56
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.55
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.54
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.53
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.52
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.51
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.51
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.5
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.49
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.48
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.48
2div_A	99	TRNA selenocysteine associated protein; structural	99.48
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.48
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.48
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.47
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.47
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.47
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.47
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.47
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.47
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.47
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.47
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.46
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.46
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.46
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.46
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.46
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.46
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.45
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.45
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.45
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.45
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.45
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.44
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.44
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.44
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.44
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.44
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.44
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.44
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.43
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.43
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.43
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.43
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.43
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.43
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.43
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.43
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.43
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.43
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.42
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.42
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.42
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.42
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.42
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.42
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.42
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.41
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.41
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.41
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.41
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.41
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.41
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.4
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.4
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.4
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.4
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.4
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.4
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.39
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.39
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.39
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.39
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.39
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.39
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.39
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.38
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.38
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.38
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.38
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.38
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.37
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.36
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.36
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.36
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.36
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.36
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.36
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.35
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.35
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.35
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.35
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.34
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.34
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.34
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.34
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.34
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.33
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.33
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.33
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.33
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.32
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.32
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.31
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.31
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.31
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.31
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.31
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.31
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.31
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.3
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.3
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.3
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.29
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.29
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.29
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.29
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.29
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.29
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.28
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.28
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.27
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.26
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.26
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.25
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.23
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.23
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.22
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.22
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.21
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.21
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.21
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.21
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.84
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.2
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.2
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.19
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.19
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.17
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.13
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.13
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.13
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.06
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.03
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.03
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.03
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.02
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.02
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.02
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.0
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.99
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.95
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.94
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.91
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.9
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.89
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.85
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.84
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.83
1x5p_A	97	Negative elongation factor E; structure genomics,	98.82
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.74
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.73
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.73
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.69
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.66
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.64
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.58
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.56
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.55
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.18
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.16
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.09
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	97.6
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	97.25
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	96.57
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	96.55
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.91
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	95.24
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	95.08
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.9
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	94.63
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	93.61
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	93.58
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.33
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	89.7
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	83.85

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

Probab=99.60  E-value=3e-15  Score=73.54  Aligned_cols=51  Identities=10%  Similarity=0.208  Sum_probs=45.3

Q ss_pred             ccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         8 ~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |........++|||+|||+.+++++|+++|++||.|.++.++.|+.|++||
T Consensus         3 ~~~~~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG   53 (103)
T 1s79_A            3 WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG   53 (103)
T ss_dssp             SCCSSCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCC
T ss_pred             ccccccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCcc
Confidence            444555567899999999999999999999999999999999998888887

>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=99.60  E-value=1.7e-15  Score=73.85  Aligned_cols=44  Identities=23%  Similarity=0.508  Sum_probs=41.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+++|||+|||..+++++|+++|++||.|.++++++|+. |++||
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG   62 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLG   62 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccc
Confidence            568999999999999999999999999999999999988 88876

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

Probab=99.56  E-value=8.5e-15  Score=72.57  Aligned_cols=45  Identities=20%  Similarity=0.313  Sum_probs=42.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +..++|||+||++.+++++|+++|++||.|.+++++.|+. |++||
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG   49 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG   49 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceee
Confidence            3568999999999999999999999999999999999998 88887

>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=99.55  E-value=1.4e-14  Score=68.63  Aligned_cols=47  Identities=32%  Similarity=0.616  Sum_probs=42.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .....++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   54 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRG   54 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCcccc
Confidence            345678999999999999999999999999999999999987 87776

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=4.7e-14  Score=68.18  Aligned_cols=48  Identities=21%  Similarity=0.463  Sum_probs=43.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        11 ~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +.....++|||+|||..+++++|+++|++||.|.+++++.|+. |+++|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   53 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRG   53 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCc
Confidence            3445778999999999999999999999999999999999987 88887

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=4.4e-14  Score=66.61  Aligned_cols=46  Identities=17%  Similarity=0.325  Sum_probs=42.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +...++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g   48 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG   48 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCc
Confidence            34678999999999999999999999999999999999987 88887

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.52  E-value=3.9e-14  Score=69.86  Aligned_cols=45  Identities=33%  Similarity=0.660  Sum_probs=40.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg   68 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG   68 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCc
Confidence            3678999999999999999999999999999999999987 88887

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.51  E-value=2e-14  Score=77.33  Aligned_cols=47  Identities=28%  Similarity=0.300  Sum_probs=40.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +....++|||||||+.+++++|+++|++||.|.++++++|+. |+++|
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G   58 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG   58 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccc
Confidence            344568999999999999999999999999999999999987 88776

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=1.2e-13  Score=66.15  Aligned_cols=46  Identities=39%  Similarity=0.632  Sum_probs=42.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++..++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g   48 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKG   48 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceee
Confidence            34678999999999999999999999999999999999987 88877

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=1.2e-13  Score=66.04  Aligned_cols=47  Identities=26%  Similarity=0.494  Sum_probs=42.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+..++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g   59 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG   59 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCccc
Confidence            445678999999999999999999999999999999999988 88877

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.49  E-value=8.2e-14  Score=67.39  Aligned_cols=48  Identities=19%  Similarity=0.326  Sum_probs=43.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEE--------EEEEeCCC-CCCCC
Q psy10283         11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPD-GTSKE   58 (59)
Q Consensus        11 ~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~--------~~v~~d~~-g~~rG   58 (59)
                      .++...++|||+|||..+++++|+++|+.||.|.+        ++++.|+. |+++|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G   64 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG   64 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeee
Confidence            34557889999999999999999999999999999        99999977 87776

>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=99.48  E-value=1.3e-13  Score=67.16  Aligned_cols=47  Identities=19%  Similarity=0.292  Sum_probs=42.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .....++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   58 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG   58 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCc
Confidence            344678999999999999999999999999999999999986 88887

>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=99.48  E-value=1.1e-13  Score=67.25  Aligned_cols=47  Identities=28%  Similarity=0.379  Sum_probs=42.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   58 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG   58 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccc
Confidence            344678999999999999999999999999999999999987 87776

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=6.6e-14  Score=67.60  Aligned_cols=47  Identities=17%  Similarity=0.288  Sum_probs=42.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeE-EEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE-ECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~-~~~v~~d~~-g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|++||.|. +++++.|+. |+++|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g   53 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAG   53 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCC
Confidence            345678999999999999999999999999999 999999986 77765

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.6e-13  Score=66.68  Aligned_cols=46  Identities=17%  Similarity=0.384  Sum_probs=42.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.++.++.++. |+++|
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   56 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG   56 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCe
Confidence            44678999999999999999999999999999999999988 88877

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

Probab=99.48  E-value=1.7e-13  Score=68.01  Aligned_cols=44  Identities=25%  Similarity=0.409  Sum_probs=41.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g   83 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC   83 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCc
Confidence            467899999999999999999999999999999999987 88887

>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=99.47  E-value=7.1e-14  Score=66.02  Aligned_cols=46  Identities=37%  Similarity=0.562  Sum_probs=39.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+..++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   49 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG   49 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccce
Confidence            34678999999999999999999999999999999999976 77665

>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=99.47  E-value=1.8e-13  Score=66.69  Aligned_cols=45  Identities=67%  Similarity=1.180  Sum_probs=40.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+++++.++.|+++|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   57 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG   57 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCc
Confidence            457899999999999999999999999999999999997776665

>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=99.47  E-value=1.6e-13  Score=66.25  Aligned_cols=46  Identities=26%  Similarity=0.379  Sum_probs=42.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   51 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG   51 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCe
Confidence            34678999999999999999999999999999999999986 88887

>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=99.47  E-value=1.6e-13  Score=67.32  Aligned_cols=46  Identities=26%  Similarity=0.460  Sum_probs=42.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.+++++.|+. |+++|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   58 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG   58 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcc
Confidence            34678999999999999999999999999999999999987 88776

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

Probab=99.47  E-value=6.8e-14  Score=64.78  Aligned_cols=42  Identities=36%  Similarity=0.699  Sum_probs=39.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g   43 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG   43 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCc
Confidence            4799999999999999999999999999999999987 88887

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.47  E-value=9.6e-15  Score=70.15  Aligned_cols=43  Identities=23%  Similarity=0.478  Sum_probs=40.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCC-CeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G-~i~~~~v~~d~~-g~~rG   58 (59)
                      +..|||+|||+.+++++|+++|++|| .|.++++++|+. |++||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg   45 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRG   45 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCc
Confidence            35799999999999999999999999 899999999988 88887

>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=99.47  E-value=6.1e-14  Score=68.44  Aligned_cols=47  Identities=36%  Similarity=0.542  Sum_probs=42.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|++||.|.+++++.|+. |+++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   56 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG   56 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcce
Confidence            344678999999999999999999999999999999999988 88887

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=2.6e-13  Score=67.20  Aligned_cols=46  Identities=35%  Similarity=0.545  Sum_probs=42.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   60 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG   60 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccce
Confidence            34678999999999999999999999999999999999987 88887

>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=99.46  E-value=1.8e-13  Score=66.87  Aligned_cols=47  Identities=13%  Similarity=0.126  Sum_probs=41.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEE-EEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE-CTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~-~~v~~d~~g~~rG   58 (59)
                      +....++|||+|||+.+++++|+++|+.||.|.+ +.++.+..|+++|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G   58 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG   58 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcce
Confidence            3446789999999999999999999999999998 8888885588887

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=9.7e-14  Score=67.68  Aligned_cols=47  Identities=26%  Similarity=0.510  Sum_probs=42.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .....++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g   59 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG   59 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcce
Confidence            345678999999999999999999999999999999999977 77765

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

Probab=99.46  E-value=6.7e-14  Score=67.93  Aligned_cols=44  Identities=7%  Similarity=0.279  Sum_probs=40.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCC--eEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGT--IEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~--i~~~~v~~d~~-g~~rG   58 (59)
                      .-.+|||+|||+.+|+++|+++|++||.  +.++++++|+. |++||
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG   54 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG   54 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSS
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCce
Confidence            4568999999999999999999999995  67899999988 99998

>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=99.46  E-value=9.1e-14  Score=65.39  Aligned_cols=46  Identities=20%  Similarity=0.426  Sum_probs=41.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   50 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG   50 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCcccc
Confidence            45678999999999999999999999999999999999866 77776

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=2.6e-13  Score=66.20  Aligned_cols=47  Identities=21%  Similarity=0.453  Sum_probs=42.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC-CC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG-PD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d-~~-g~~rG   58 (59)
                      .....++|||+|||..+++++|+++|+.||.|.+++++.+ +. |+++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g   59 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG   59 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCS
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCc
Confidence            3446789999999999999999999999999999999999 55 88776

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.46  E-value=5.8e-14  Score=71.02  Aligned_cols=45  Identities=13%  Similarity=0.310  Sum_probs=41.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEE--EEEEeCCC-CCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--CTVLKGPD-GTSKER   59 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~--~~v~~d~~-g~~rG~   59 (59)
                      ..++|||+|||+.+++++|+++|++||.|..  +++++|+. |++||.
T Consensus        22 ~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~   69 (131)
T 2m2b_A           22 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGF   69 (131)
T ss_dssp             CCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceE
Confidence            5679999999999999999999999999977  99999997 999883

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.8e-13  Score=66.49  Aligned_cols=46  Identities=30%  Similarity=0.497  Sum_probs=41.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   58 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG   58 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceee
Confidence            34678999999999999999999999999999999999976 77765

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

Probab=99.45  E-value=2.8e-13  Score=65.54  Aligned_cols=46  Identities=20%  Similarity=0.361  Sum_probs=41.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.+++++.++.|+++|
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   59 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG   59 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEe
Confidence            3467899999999999999999999999999999999988776665

>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=99.45  E-value=1.3e-13  Score=66.12  Aligned_cols=46  Identities=26%  Similarity=0.474  Sum_probs=41.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.++.|+++|
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   58 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS   58 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCce
Confidence            3467899999999999999999999999999999999998776665

>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=99.45  E-value=2.8e-13  Score=64.17  Aligned_cols=43  Identities=19%  Similarity=0.388  Sum_probs=40.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   49 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG   49 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcce
Confidence            47899999999999999999999999999999999986 88776

>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=99.45  E-value=2.2e-13  Score=65.58  Aligned_cols=43  Identities=19%  Similarity=0.457  Sum_probs=40.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   45 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG   45 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccce
Confidence            57899999999999999999999999999999999987 88776

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.8e-13  Score=65.49  Aligned_cols=46  Identities=26%  Similarity=0.366  Sum_probs=41.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +...++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g   58 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG   58 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccc
Confidence            34678999999999999999999999999999999999987 77665

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2e-13  Score=66.18  Aligned_cols=47  Identities=34%  Similarity=0.554  Sum_probs=42.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .....++|||+|||..+++++|+++|++||.|.+++++.++. ++++|
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   55 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG   55 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCccc
Confidence            345678999999999999999999999999999999999987 88776

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=3.6e-13  Score=66.39  Aligned_cols=46  Identities=20%  Similarity=0.341  Sum_probs=41.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.++.|+++|
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g   57 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG   57 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeee
Confidence            3457899999999999999999999999999999999997776665

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.44  E-value=3.4e-13  Score=68.28  Aligned_cols=45  Identities=27%  Similarity=0.392  Sum_probs=41.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+++++.|+. |+++|
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G   89 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG   89 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccce
Confidence            4578999999999999999999999999999999999987 88887

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2.2e-13  Score=66.03  Aligned_cols=46  Identities=20%  Similarity=0.426  Sum_probs=42.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.|+. |+++|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   55 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG   55 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcce
Confidence            34678999999999999999999999999999999999977 88876

>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=99.44  E-value=1.9e-13  Score=67.61  Aligned_cols=45  Identities=27%  Similarity=0.511  Sum_probs=41.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   68 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC   68 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCc
Confidence            3568999999999999999999999999999999999986 77765

>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=99.44  E-value=2.3e-13  Score=63.73  Aligned_cols=42  Identities=26%  Similarity=0.419  Sum_probs=38.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g   44 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG   44 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccc
Confidence            5899999999999999999999999999999999976 77765

>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=99.43  E-value=9.7e-14  Score=68.93  Aligned_cols=39  Identities=23%  Similarity=0.489  Sum_probs=35.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ...+|||+|||+.+++++|+++|++||.|.+++|+.|..
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~   42 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN   42 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC
Confidence            456899999999999999999999999999999999864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=2.9e-13  Score=65.78  Aligned_cols=47  Identities=23%  Similarity=0.383  Sum_probs=41.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhcc-CCCeEEEEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAP-FGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~-~G~i~~~~v~~d~~g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|+. ||.|.+++++.|+.|+++|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g   52 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKG   52 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccc
Confidence            3456789999999999999999999999 9999999999997776665

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.43  E-value=3.9e-14  Score=68.90  Aligned_cols=45  Identities=13%  Similarity=0.175  Sum_probs=41.8

Q ss_pred             CCCCeEEEcCCCC------CCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSK------QQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~------~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+++|||+|||.      .+++++|+++|++||.|.+++++.|+. |++||
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG   55 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKG   55 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccce
Confidence            3467899999999      999999999999999999999999998 88887

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.43  E-value=9.7e-14  Score=64.09  Aligned_cols=41  Identities=27%  Similarity=0.556  Sum_probs=38.6

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   42 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG   42 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCB
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCc
Confidence            589999999999999999999999999999999987 88887

>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=99.43  E-value=2.4e-13  Score=66.99  Aligned_cols=45  Identities=38%  Similarity=0.620  Sum_probs=40.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +..++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   69 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG   69 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccce
Confidence            4678999999999999999999999999999999999876 77665

>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=99.43  E-value=6.8e-14  Score=66.79  Aligned_cols=42  Identities=24%  Similarity=0.412  Sum_probs=38.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCC--CeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G--~i~~~~v~~d~~-g~~rG   58 (59)
                      .+|||+|||+.+++++|+++|++||  .|.+++++.|+. |++||
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG   46 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG   46 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCc
Confidence            4799999999999999999999999  999999999987 88876

>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=99.43  E-value=5.1e-13  Score=65.88  Aligned_cols=46  Identities=22%  Similarity=0.508  Sum_probs=41.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.+++++.++.|+++|
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g   67 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG   67 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcce
Confidence            3467899999999999999999999999999999999997666665

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.43  E-value=9.3e-14  Score=70.99  Aligned_cols=43  Identities=12%  Similarity=0.261  Sum_probs=41.2

Q ss_pred             CeEEEcCC----CCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         17 KKLFVGML----SKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        17 ~~l~v~~L----~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      .+|||+||    |+.+++..|+.+|+.||+|.++.++.|+. |+++|+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGf   50 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHV   50 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeE
Confidence            68999999    99999999999999999999999999999 999984

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.43  E-value=1.7e-13  Score=71.40  Aligned_cols=44  Identities=18%  Similarity=0.326  Sum_probs=40.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCC--CeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G--~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||+.+++++|+++|+.||  .|.+++++.|+. |++||
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skG  100 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKG  100 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccce
Confidence            357999999999999999999999999  999999999987 88876

>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=99.43  E-value=4.8e-13  Score=66.04  Aligned_cols=43  Identities=16%  Similarity=0.397  Sum_probs=40.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|+.||.|.+++++.|+. |+++|
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   68 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG   68 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCc
Confidence            46899999999999999999999999999999999988 88887

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.42  E-value=1.3e-13  Score=70.62  Aligned_cols=46  Identities=9%  Similarity=0.014  Sum_probs=41.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCC---eEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGT---IEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~---i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||+++++++|+++|++||.   |.+++++.|+.|++||
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG   89 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSG   89 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCe
Confidence            345789999999999999999999999999   8999999998888876

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.42  E-value=4.1e-13  Score=66.31  Aligned_cols=46  Identities=37%  Similarity=0.611  Sum_probs=41.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   58 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG   58 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcce
Confidence            34678999999999999999999999999999999999976 77665

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=3.2e-13  Score=66.01  Aligned_cols=45  Identities=20%  Similarity=0.376  Sum_probs=39.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +...++|||+|||+.+++++|+++|++||. .+++++.|+.|++||
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G   56 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTG   56 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEee
Confidence            446789999999999999999999999995 599999998787776

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=3e-13  Score=67.03  Aligned_cols=47  Identities=11%  Similarity=0.051  Sum_probs=42.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCe-EEEEEEeCCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTI-EECTVLKGPDGTSKER   59 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i-~~~~v~~d~~g~~rG~   59 (59)
                      +...++|||+|||+.+++++|+++|+.||.| .+++++.|+.|+++|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~   59 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ   59 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSC
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceE
Confidence            3467899999999999999999999999999 8899999988888873

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=3.4e-13  Score=65.78  Aligned_cols=44  Identities=25%  Similarity=0.361  Sum_probs=40.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.|+. |+++|
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   66 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG   66 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceee
Confidence            457899999999999999999999999999999999987 77765

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

Probab=99.42  E-value=4.8e-13  Score=66.22  Aligned_cols=43  Identities=30%  Similarity=0.685  Sum_probs=40.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|+.||.|.++.++.++. |+++|
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   70 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG   70 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCc
Confidence            47899999999999999999999999999999999987 88887

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.42  E-value=4.6e-13  Score=65.37  Aligned_cols=46  Identities=28%  Similarity=0.455  Sum_probs=41.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.+..|+++|
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   71 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG   71 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcce
Confidence            3457899999999999999999999999999999999998776665

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

Probab=99.41  E-value=6.3e-13  Score=67.28  Aligned_cols=44  Identities=20%  Similarity=0.453  Sum_probs=41.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g  106 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG  106 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCS
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCc
Confidence            577999999999999999999999999999999999977 88887

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.41  E-value=6.1e-13  Score=66.20  Aligned_cols=45  Identities=29%  Similarity=0.518  Sum_probs=41.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.++.++.+..|+++|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   49 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG   49 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCccc
Confidence            457899999999999999999999999999999999988777776

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

Probab=99.41  E-value=4e-13  Score=65.94  Aligned_cols=44  Identities=25%  Similarity=0.413  Sum_probs=40.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.++. |+++|
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   69 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG   69 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcce
Confidence            567899999999999999999999999999999999987 88877

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=2.7e-13  Score=65.05  Aligned_cols=45  Identities=29%  Similarity=0.584  Sum_probs=41.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEE-EEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~-~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|++||.|.++ +++.|+. |+++|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g   49 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKG   49 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCe
Confidence            357899999999999999999999999999999 9999976 88877

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.41  E-value=7.5e-13  Score=67.11  Aligned_cols=44  Identities=16%  Similarity=0.210  Sum_probs=39.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeE--EEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE--ECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~--~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||+.+++++|+++|+.| .|.  +++++.|+.|++||
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrG   85 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITG   85 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCce
Confidence            356889999999999999999999999 677  89999998898887

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=2.1e-12  Score=62.69  Aligned_cols=46  Identities=26%  Similarity=0.465  Sum_probs=40.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      .....++|||+|||..+++++|+++|+.||.|.+++++.+..+ ++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g   56 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKG   56 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcE
Confidence            3446789999999999999999999999999999999988653 454

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.40  E-value=7.6e-13  Score=64.34  Aligned_cols=46  Identities=24%  Similarity=0.421  Sum_probs=41.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|+.|| |.+++++.|+. |+++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g   57 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKG   57 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccce
Confidence            344678999999999999999999999997 99999999987 87776

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.40  E-value=4.2e-13  Score=69.13  Aligned_cols=44  Identities=32%  Similarity=0.675  Sum_probs=41.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   46 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRG   46 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccc
Confidence            357899999999999999999999999999999999987 88887

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.40  E-value=2.3e-13  Score=67.89  Aligned_cols=46  Identities=9%  Similarity=0.045  Sum_probs=41.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCC---eEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGT---IEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~---i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||+.+++++|+++|+.||.   |.+++++.|+.|+++|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G   62 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG   62 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCe
Confidence            345788999999999999999999999999   8999999998888776

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.40  E-value=9.8e-13  Score=65.80  Aligned_cols=45  Identities=29%  Similarity=0.441  Sum_probs=41.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+++++.++.|+++|
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g   77 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG   77 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEee
Confidence            356799999999999999999999999999999999988777776

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.40  E-value=2.5e-13  Score=65.91  Aligned_cols=45  Identities=20%  Similarity=0.400  Sum_probs=38.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC-C-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP-D-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~-~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.|| |.+++++.++ . |+++|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g   62 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG   62 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCe
Confidence            34678999999999999999999999999 9999999998 4 88887

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=9.5e-13  Score=63.92  Aligned_cols=45  Identities=33%  Similarity=0.518  Sum_probs=39.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.+ .|+++|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g   56 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG   56 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCE
Confidence            446789999999999999999999999999999999988 555554

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.39  E-value=1.3e-13  Score=63.59  Aligned_cols=41  Identities=29%  Similarity=0.532  Sum_probs=38.6

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   42 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG   42 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCC
Confidence            589999999999999999999999999999999987 88887

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.39  E-value=2.4e-13  Score=66.75  Aligned_cols=47  Identities=15%  Similarity=0.073  Sum_probs=42.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCC---eEEEEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGT---IEECTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~---i~~~~v~~d~~g~~rG   58 (59)
                      +....++|||+|||+.+++++|+++|+.||.   |.+++++.|+.|+++|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G   56 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRG   56 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEee
Confidence            3456789999999999999999999999998   8999999998888887

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.39  E-value=3.3e-13  Score=69.37  Aligned_cols=43  Identities=21%  Similarity=0.389  Sum_probs=39.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..++|||+|||+++++++|+++|++|| +.+++++.|++|++||
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srG   87 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTG   87 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCce
Confidence            567899999999999999999999999 7799999998888887

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.39  E-value=9.1e-13  Score=65.95  Aligned_cols=44  Identities=25%  Similarity=0.361  Sum_probs=40.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.++. |+++|
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   65 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG   65 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccce
Confidence            567999999999999999999999999999999999986 88776

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.39  E-value=4.2e-13  Score=70.60  Aligned_cols=46  Identities=30%  Similarity=0.649  Sum_probs=42.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +...++|||+|||..+++++|+++|+.||.|.++.++.++. |+++|
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   56 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG   56 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccc
Confidence            34678999999999999999999999999999999999987 87776

>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=99.39  E-value=7.1e-13  Score=63.37  Aligned_cols=39  Identities=18%  Similarity=0.447  Sum_probs=34.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .....+|||+|||+++++++|+++|++||.|.+++++.+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~   46 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP   46 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC
Confidence            446789999999999999999999999999999999876

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.3e-12  Score=63.59  Aligned_cols=46  Identities=22%  Similarity=0.434  Sum_probs=40.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC--CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD--GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~--g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|+.|| |.++.++.++.  |+++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g   58 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG   58 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCS
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCe
Confidence            334678999999999999999999999999 99999999876  67776

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

Probab=99.38  E-value=6.5e-13  Score=65.61  Aligned_cols=41  Identities=24%  Similarity=0.408  Sum_probs=37.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .+...++|||+|||+.+++++|+++|++||.|.+++++.++
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~k   52 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK   52 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCC
Confidence            34568899999999999999999999999999999998763

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.38  E-value=6.5e-13  Score=68.57  Aligned_cols=44  Identities=18%  Similarity=0.332  Sum_probs=41.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.|+. |+++|
T Consensus        69 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g  113 (158)
T 2kn4_A           69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG  113 (158)
T ss_dssp             BCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccce
Confidence            468999999999999999999999999999999999986 88887

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.38  E-value=3.7e-13  Score=68.33  Aligned_cols=44  Identities=20%  Similarity=0.427  Sum_probs=40.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   85 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG   85 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcce
Confidence            568999999999999999999999999999999999987 77665

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.38  E-value=5.6e-13  Score=64.66  Aligned_cols=44  Identities=27%  Similarity=0.597  Sum_probs=40.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.|+.|+++|
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   51 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG   51 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccc
Confidence            46799999999999999999999999999999999997676665

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=4e-13  Score=66.58  Aligned_cols=43  Identities=23%  Similarity=0.307  Sum_probs=39.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ...+|||+|||+.+++++|+++|+.| .|.+++++.|+.|+++|
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G   57 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNG   57 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCe
Confidence            34689999999999999999999999 89999999998898887

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.37  E-value=7.1e-13  Score=72.49  Aligned_cols=44  Identities=23%  Similarity=0.387  Sum_probs=39.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCC--CeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G--~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+||++.+++++|+++|+.||  .|.+++|++|+. |++||
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skG  113 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG  113 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccce
Confidence            456899999999999999999999999  999999999987 88876

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=1.2e-12  Score=64.44  Aligned_cols=45  Identities=18%  Similarity=0.358  Sum_probs=41.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeE--------EEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE--------ECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~--------~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.        .++++.|+. |+++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g   66 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG   66 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeee
Confidence            4678999999999999999999999999999        699999976 88877

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.36  E-value=6.3e-13  Score=66.37  Aligned_cols=43  Identities=23%  Similarity=0.420  Sum_probs=39.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   79 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG   79 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCccc
Confidence            56899999999999999999999999999999999976 87776

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

Probab=99.36  E-value=1.4e-13  Score=65.46  Aligned_cols=42  Identities=19%  Similarity=0.497  Sum_probs=39.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   44 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG   44 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcce
Confidence            5799999999999999999999999999999999987 88876

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

Probab=99.36  E-value=1.4e-12  Score=64.17  Aligned_cols=44  Identities=25%  Similarity=0.438  Sum_probs=38.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|++||.|.+++++.+.. +++|
T Consensus        27 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg   70 (109)
T 2err_A           27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKG   70 (109)
T ss_dssp             TCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCce
Confidence            3678999999999999999999999999999999998864 3555

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

Probab=99.36  E-value=2e-12  Score=61.58  Aligned_cols=46  Identities=17%  Similarity=0.159  Sum_probs=39.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +....++|||+|||..+++++|+++|++||.|.+++++.+ .|+++|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g   49 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKG   49 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcce
Confidence            3456789999999999999999999999999999999885 355554

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

Probab=99.36  E-value=6.3e-13  Score=67.71  Aligned_cols=44  Identities=18%  Similarity=0.332  Sum_probs=41.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G   90 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG   90 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccce
Confidence            567899999999999999999999999999999999987 88887

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.35  E-value=2e-12  Score=66.75  Aligned_cols=44  Identities=23%  Similarity=0.265  Sum_probs=40.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|.++.++.++. ++++|
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   82 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG   82 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccce
Confidence            568999999999999999999999999999999999987 77665

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=7.2e-13  Score=66.87  Aligned_cols=45  Identities=18%  Similarity=0.197  Sum_probs=39.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCe----EEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTI----EECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i----~~~~v~~d~~g~~rG   58 (59)
                      ....+|||+|||+++++++|+++|++||.|    .++.++.|..|+++|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G   69 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG   69 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEee
Confidence            356799999999999999999999999875    689999996688876

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=1.8e-12  Score=62.44  Aligned_cols=43  Identities=12%  Similarity=0.189  Sum_probs=38.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHH----HhhccCCCeEEEEEEeCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLKGPDG   54 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~----~~F~~~G~i~~~~v~~d~~g   54 (59)
                      +....++|||+|||..+++++|+    ++|++||.|.+++++.|+.+
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~   51 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY   51 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC
Confidence            44567899999999999999999    99999999999999988754

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=1.2e-12  Score=64.03  Aligned_cols=45  Identities=16%  Similarity=0.324  Sum_probs=40.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCC-eEEEEEE-eCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVL-KGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~-i~~~~v~-~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||. |.++.++ .+.. |+++|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g   53 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRG   53 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCc
Confidence            45789999999999999999999999998 9999988 6766 78877

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.34  E-value=1.1e-12  Score=61.87  Aligned_cols=44  Identities=23%  Similarity=0.382  Sum_probs=38.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CC-CCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GT-SKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~-~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|.++.++.+.. +. ++|
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g   48 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG   48 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCc
Confidence            467999999999999999999999999999999998876 33 555

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=2.5e-12  Score=61.21  Aligned_cols=47  Identities=11%  Similarity=0.146  Sum_probs=41.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        11 ~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      .+....++|||+|||..+++++|+++|+.| .|.+++++.+..|+++|
T Consensus         5 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g   51 (91)
T 2dgw_A            5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTG   51 (91)
T ss_dssp             CCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEE
T ss_pred             CCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCce
Confidence            344567899999999999999999999999 99999999995587776

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.34  E-value=2.1e-12  Score=60.47  Aligned_cols=42  Identities=26%  Similarity=0.383  Sum_probs=36.2

Q ss_pred             CCeEEEcCCCCCC------cHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQ------NEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~------~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +++|||+|||..+      ++++|+++|++||.|.++.++ ...|+++|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g   48 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKG   48 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeE
Confidence            3689999999999      779999999999999999877 33378777

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=6.5e-13  Score=64.50  Aligned_cols=44  Identities=20%  Similarity=0.477  Sum_probs=39.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g   51 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG   51 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccce
Confidence            457899999999999999999999999999999999976 77665

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.34  E-value=2.5e-12  Score=63.15  Aligned_cols=39  Identities=13%  Similarity=0.284  Sum_probs=35.8

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ...++|||+|||+ .+++++|+++|++||.|.++.++.++
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k   52 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI   52 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC
Confidence            3578999999999 99999999999999999999998764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.33  E-value=1.8e-12  Score=64.16  Aligned_cols=44  Identities=25%  Similarity=0.400  Sum_probs=38.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC----CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD----GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~----g~~rG   58 (59)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.+..    |++||
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G   53 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKG   53 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCccc
Confidence            4578999999999999999999999999999 77777765    46776

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.33  E-value=3.5e-13  Score=64.93  Aligned_cols=46  Identities=17%  Similarity=0.205  Sum_probs=40.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.||.|.++.++.++. |+++|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g   58 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG   58 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeee
Confidence            34568899999999999999999999999999888888766 77665

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=4.6e-12  Score=61.46  Aligned_cols=45  Identities=20%  Similarity=0.411  Sum_probs=39.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.++.+ ++|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g   56 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDP   56 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCC
Confidence            346789999999999999999999999999999999998653 344

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.33  E-value=4.1e-12  Score=65.66  Aligned_cols=55  Identities=33%  Similarity=0.611  Sum_probs=45.9

Q ss_pred             eeecccCC--CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          4 LDLIWNCT--PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         4 ~~~~~~~~--~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +++.++..  +....++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        80 i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g  137 (172)
T 2g4b_A           80 LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG  137 (172)
T ss_dssp             CEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEE
T ss_pred             eeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcce
Confidence            45555554  234578999999999999999999999999999999999975 87776

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.32  E-value=1.8e-12  Score=62.37  Aligned_cols=40  Identities=25%  Similarity=0.527  Sum_probs=36.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ...++|||+|||..+++++|+++|++||.|.++.++.++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   42 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN   42 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            3568999999999999999999999999999999998764

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

Probab=99.32  E-value=5.8e-12  Score=61.74  Aligned_cols=38  Identities=21%  Similarity=0.296  Sum_probs=35.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      +.++.|||+|||+.+++++|+++|++||.|.++.++++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~   56 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK   56 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC
Confidence            45789999999999999999999999999999998764

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.31  E-value=1.8e-12  Score=67.04  Aligned_cols=44  Identities=32%  Similarity=0.596  Sum_probs=39.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-C--CCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-G--TSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g--~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|.+++++.++. |  +++|
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g   48 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG   48 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcce
Confidence            467999999999999999999999999999999999987 4  5555

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=5.4e-13  Score=66.84  Aligned_cols=46  Identities=11%  Similarity=0.164  Sum_probs=38.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||+.+++++|+++|+.||.|.++.++.+.. |+++|
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G   68 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG   68 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCe
Confidence            34668999999999999999999999999998855555544 77766

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.31  E-value=3.8e-12  Score=65.30  Aligned_cols=43  Identities=26%  Similarity=0.571  Sum_probs=39.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g   45 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG   45 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCccee
Confidence            57899999999999999999999999999999999985 87766

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.31  E-value=3e-12  Score=66.18  Aligned_cols=56  Identities=45%  Similarity=0.870  Sum_probs=45.3

Q ss_pred             ceeecccCCCCC---CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          3 PLDLIWNCTPLP---PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~~---~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ++.+.++.....   ..++|||+|||..+++++|+++|++||.|.+++++.++.|+++|
T Consensus        79 ~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g  137 (175)
T 3nmr_A           79 PIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRG  137 (175)
T ss_dssp             CCEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEE
T ss_pred             ceEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEE
Confidence            344444444222   56799999999999999999999999999999999997777765

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.31  E-value=7.3e-12  Score=64.16  Aligned_cols=56  Identities=21%  Similarity=0.373  Sum_probs=46.1

Q ss_pred             ceeecccCCC----CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          3 PLDLIWNCTP----LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~----~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++++.|+...    ....++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        70 ~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g  130 (166)
T 3md3_A           70 IVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG  130 (166)
T ss_dssp             ECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEE
T ss_pred             eeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcce
Confidence            3455565443    23567899999999999999999999999999999999976 77765

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.31  E-value=4.1e-13  Score=64.31  Aligned_cols=45  Identities=18%  Similarity=0.228  Sum_probs=38.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +..++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g   58 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG   58 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEee
Confidence            3468999999999999999999999999999888888776 77665

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.31  E-value=4.4e-12  Score=66.13  Aligned_cols=44  Identities=25%  Similarity=0.413  Sum_probs=39.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++. |+++|
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g  115 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG  115 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEee
Confidence            456899999999999999999999999999999999976 77765

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.30  E-value=6.3e-12  Score=61.42  Aligned_cols=43  Identities=26%  Similarity=0.354  Sum_probs=37.5

Q ss_pred             CCCeEEEcCCCCCC------cHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQ------NEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~------~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..++|||+|||..+      ++++|+++|++||.|.++.++ ...|+++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G   62 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKG   62 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCC
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeee
Confidence            46799999999999      789999999999999999988 33388877

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.30  E-value=4.9e-12  Score=63.61  Aligned_cols=38  Identities=26%  Similarity=0.480  Sum_probs=35.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      +..++|||+|||+.+++++|+++|++||.|.++.++.+
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~   66 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG   66 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC
Confidence            35788999999999999999999999999999999876

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.30  E-value=1e-11  Score=60.90  Aligned_cols=39  Identities=13%  Similarity=0.195  Sum_probs=35.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ....++|||+|||+.+++++|+++|++||.|.++.++.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~   50 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   50 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC
Confidence            346789999999999999999999999999999998875

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.29  E-value=3e-12  Score=65.89  Aligned_cols=44  Identities=20%  Similarity=0.505  Sum_probs=40.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g   46 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG   46 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccce
Confidence            467999999999999999999999999999999999876 87776

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.29  E-value=4.9e-12  Score=59.92  Aligned_cols=38  Identities=24%  Similarity=0.510  Sum_probs=35.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||..+++++|+++|++||.|.+++++.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~   40 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP   40 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC
Confidence            35689999999999999999999999999999998876

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.29  E-value=2.2e-12  Score=66.17  Aligned_cols=42  Identities=24%  Similarity=0.400  Sum_probs=38.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ++|||+|||..+++++|+++|+.||.|.+++++.++.|+++|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g   42 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN   42 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCC
Confidence            579999999999999999999999999999999998777765

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.29  E-value=7.8e-12  Score=65.73  Aligned_cols=44  Identities=27%  Similarity=0.558  Sum_probs=40.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.|+. |+++|
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g  147 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG  147 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccc
Confidence            357899999999999999999999999999999999986 77776

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

Probab=99.29  E-value=6.6e-12  Score=66.44  Aligned_cols=45  Identities=29%  Similarity=0.443  Sum_probs=41.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER   59 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG~   59 (59)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.+..|+++|.
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~  131 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT  131 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeE
Confidence            467999999999999999999999999999999999887777763

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.29  E-value=1.3e-11  Score=63.54  Aligned_cols=56  Identities=21%  Similarity=0.408  Sum_probs=46.8

Q ss_pred             ceeecccCCC--CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          3 PLDLIWNCTP--LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~--~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++++.|+.+.  ....++|||+|||..+++++|+++|++||.|.++.++.+.. |+++|
T Consensus        74 ~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g  132 (168)
T 1b7f_A           74 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG  132 (168)
T ss_dssp             ECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEE
T ss_pred             EEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcce
Confidence            3556666653  33578999999999999999999999999999999999985 77665

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=1.2e-11  Score=60.47  Aligned_cols=38  Identities=29%  Similarity=0.523  Sum_probs=35.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      +..++|||+|||+.+++++|+++|++||.|.++.++.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~   50 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG   50 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC
Confidence            35689999999999999999999999999999988875

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.28  E-value=1.9e-11  Score=60.05  Aligned_cols=37  Identities=22%  Similarity=0.189  Sum_probs=34.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..++|||+|||..+++++|+++|++||.|.++.++.+
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~   50 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF   50 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC
Confidence            5689999999999999999999999999999988765

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.27  E-value=1.9e-11  Score=60.25  Aligned_cols=41  Identities=22%  Similarity=0.462  Sum_probs=37.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ++...++|||+|||..+++++|+++|+.||.|.++.++.+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~   44 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP   44 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC
Confidence            44567899999999999999999999999999999998764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.27  E-value=1.1e-11  Score=63.48  Aligned_cols=56  Identities=20%  Similarity=0.397  Sum_probs=46.4

Q ss_pred             ceeecccCCCC--CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283          3 PLDLIWNCTPL--PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~--~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++++.|+.+..  ...++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        73 ~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g  131 (167)
T 1fxl_A           73 TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG  131 (167)
T ss_dssp             ECEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             eEEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccc
Confidence            35566665532  3578899999999999999999999999999999999986 77665

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

Probab=99.26  E-value=1.1e-11  Score=66.00  Aligned_cols=43  Identities=28%  Similarity=0.457  Sum_probs=38.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g   71 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG   71 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCc
Confidence            56899999999999999999999999999999999986 88877

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.26  E-value=1e-11  Score=61.18  Aligned_cols=41  Identities=22%  Similarity=0.377  Sum_probs=37.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHH---HhhccCCCeEEEEEEeCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVR---KIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~---~~F~~~G~i~~~~v~~d~~   53 (59)
                      ....++|||+|||+.+++++|+   ++|++||.|.++.++.+..
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~   55 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS   55 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSS
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCC
Confidence            3457899999999999999999   9999999999999998875

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.25  E-value=1.2e-11  Score=66.19  Aligned_cols=43  Identities=9%  Similarity=0.225  Sum_probs=39.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      .++|||+|||+.+++++|+++|++||.|.+++++.+..|+++|
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG  151 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG  151 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEE
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCccc
Confidence            4789999999999999999999999999999999987777776

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.24  E-value=1.7e-11  Score=58.46  Aligned_cols=40  Identities=28%  Similarity=0.536  Sum_probs=35.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .....++|||+|||..+++++|+++|++||.|.++.++++
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~   45 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD   45 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC
Confidence            3456789999999999999999999999999999988643

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.23  E-value=2.9e-11  Score=63.61  Aligned_cols=45  Identities=31%  Similarity=0.606  Sum_probs=40.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|++||.|.++.++.++. |+++|
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g  157 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG  157 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcce
Confidence            3568999999999999999999999999999999999975 77665

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

Probab=99.23  E-value=1.4e-11  Score=58.54  Aligned_cols=40  Identities=30%  Similarity=0.510  Sum_probs=35.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .....++|||+|||..+++++|+++|++||.|.+++++++
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~   44 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD   44 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC
Confidence            3456789999999999999999999999999999988754

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

Probab=99.23  E-value=3.3e-11  Score=64.13  Aligned_cols=44  Identities=25%  Similarity=0.632  Sum_probs=40.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.+.. |+++|
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g  168 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG  168 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCc
Confidence            457999999999999999999999999999999999976 77765

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=3.1e-11  Score=56.62  Aligned_cols=39  Identities=33%  Similarity=0.462  Sum_probs=35.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~   47 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR   47 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC
Confidence            346789999999999999999999999999999998864

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.22  E-value=2.6e-11  Score=71.32  Aligned_cols=44  Identities=23%  Similarity=0.428  Sum_probs=40.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|.++|+.||.|..|.|+.|.. |+++|
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG  145 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG  145 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccc
Confidence            357999999999999999999999999999999999976 88876

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=3.1e-11  Score=58.33  Aligned_cols=43  Identities=26%  Similarity=0.338  Sum_probs=36.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|   +++.+..|+++|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g   54 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKG   54 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEee
Confidence            4467899999999999999999999999987   566664477776

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.21  E-value=9.9e-12  Score=59.56  Aligned_cols=41  Identities=15%  Similarity=0.315  Sum_probs=36.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEE-EEeCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECT-VLKGPD   53 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~-v~~d~~   53 (59)
                      ....++|||+|||..+++++|+++|+.||.|.+++ ++.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~   53 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE   53 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC
Confidence            34578999999999999999999999999999994 777764

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

Probab=99.21  E-value=4.4e-11  Score=56.79  Aligned_cols=38  Identities=29%  Similarity=0.693  Sum_probs=34.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      +....++|||+|||..+++++|+++|++||.|.++.++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~   41 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII   41 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE
Confidence            34577899999999999999999999999999999886

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.21  E-value=4.9e-11  Score=57.29  Aligned_cols=39  Identities=28%  Similarity=0.508  Sum_probs=35.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ....++|||+|||..+++++|+++|++||.|.++.+..+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~   52 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG   52 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC
Confidence            345789999999999999999999999999999988765

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.84  E-value=1.4e-12  Score=64.63  Aligned_cols=45  Identities=20%  Similarity=0.361  Sum_probs=40.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEE--------EEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~--------~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+        ++++.|+. |+++|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g   58 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG   58 (116)
Confidence            35679999999999999999999999999999        88999877 77776

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.20  E-value=4.3e-11  Score=60.60  Aligned_cols=43  Identities=9%  Similarity=0.216  Sum_probs=35.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHH----HhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~----~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||+.+++++|+    ++|++||.|.++.+..  .|++||
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG   73 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSG   73 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCC
Confidence            357899999999999998866    6999999999987753  366776

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.20  E-value=5.8e-11  Score=57.22  Aligned_cols=40  Identities=30%  Similarity=0.581  Sum_probs=35.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ....++|||+|||..+++++|+++|++||.|.+++++.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~k   51 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK   51 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCC
Confidence            3467899999999999999999999999999999988653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=1.1e-10  Score=55.86  Aligned_cols=38  Identities=16%  Similarity=0.371  Sum_probs=33.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ...++|||+|||..+++++|+++|++||.|.++  +.++.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~   43 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKD   43 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCC
Confidence            356799999999999999999999999999987  55554

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.19  E-value=2.2e-11  Score=60.66  Aligned_cols=38  Identities=16%  Similarity=0.364  Sum_probs=34.6

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~-~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||++ +++++|+++|++||.|.++.++++
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~   61 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM   61 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC
Confidence            35789999999998 999999999999999999998754

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=7.5e-11  Score=57.69  Aligned_cols=38  Identities=21%  Similarity=0.490  Sum_probs=34.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||..+++++|+++|++||.|.++++..+
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~   57 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR   57 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC
Confidence            35689999999999999999999999999999998655

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.18  E-value=3.3e-11  Score=66.40  Aligned_cols=51  Identities=22%  Similarity=0.349  Sum_probs=43.7

Q ss_pred             eeecccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          4 LDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         4 ~~~~~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +++.|+.+    ..+|||+|||..+++++|+++|+.||.|.++.++.|..|+++|
T Consensus        88 l~v~~a~~----~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g  138 (261)
T 3sde_A           88 LRIRFATH----GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG  138 (261)
T ss_dssp             CEEEECCC----SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEE
T ss_pred             eEeeeccc----CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCc
Confidence            45555543    5689999999999999999999999999999999996687776

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.17  E-value=8.3e-11  Score=56.80  Aligned_cols=37  Identities=22%  Similarity=0.401  Sum_probs=34.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      ...++|||+|||..+++++|+++|+.||.|.++++..
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~   61 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP   61 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec
Confidence            4578999999999999999999999999999999874

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.15  E-value=1.7e-11  Score=63.08  Aligned_cols=44  Identities=25%  Similarity=0.516  Sum_probs=40.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||.|.+++++.++. |+++|
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g  130 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRG  130 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSE
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccce
Confidence            466899999999999999999999999999999999977 88887

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.14  E-value=7.8e-11  Score=57.18  Aligned_cols=38  Identities=34%  Similarity=0.489  Sum_probs=34.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||..+++++|+++|++||.|.++.++++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~   46 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD   46 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC
Confidence            35689999999999999999999999999999988643

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.14  E-value=5.3e-11  Score=61.06  Aligned_cols=38  Identities=26%  Similarity=0.555  Sum_probs=35.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||+.+++++|+++|++||.|.+++++.+
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~  108 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN  108 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC
Confidence            35689999999999999999999999999999999887

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.13  E-value=7.5e-11  Score=57.73  Aligned_cols=38  Identities=26%  Similarity=0.552  Sum_probs=35.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||..+++++|+++|+.||.|.+++++.+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~   60 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE   60 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC
Confidence            46789999999999999999999999999999999876

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.13  E-value=2.6e-11  Score=60.22  Aligned_cols=47  Identities=9%  Similarity=-0.018  Sum_probs=34.1

Q ss_pred             ceeecccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCC-CeEEEEEEe
Q psy10283          3 PLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLK   50 (59)
Q Consensus         3 ~~~~~~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G-~i~~~~v~~   50 (59)
                      ++++.+... +....+|||+|||+.+++++|+++|++|| .|..+.+..
T Consensus        16 ~~~~~~~~~-p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~   63 (111)
T 2jvr_A           16 PRGSHMSKL-PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT   63 (111)
T ss_dssp             ----------CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS
T ss_pred             ecchhcCCC-CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc
Confidence            344555544 34678999999999999999999999999 899988754

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.13  E-value=3e-11  Score=59.92  Aligned_cols=38  Identities=13%  Similarity=0.219  Sum_probs=33.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||+|||..+++++|+++|++||.|.++.++.+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~   51 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   51 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC
Confidence            35689999999999999999999999999999998765

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.13  E-value=1.4e-10  Score=55.98  Aligned_cols=38  Identities=26%  Similarity=0.545  Sum_probs=33.7

Q ss_pred             CCCCCCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEE
Q psy10283         12 PLPPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      +.+..++|||+|||. .+++++|+++|+.||.|.++++.
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            344688999999998 99999999999999999999873

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.13  E-value=1.5e-12  Score=63.00  Aligned_cols=43  Identities=14%  Similarity=0.285  Sum_probs=37.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.. .++.+.. |+++|
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g   59 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRK   59 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCc
Confidence            5779999999999999999999999999888 6666655 77776

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

Probab=99.12  E-value=1.4e-10  Score=56.98  Aligned_cols=36  Identities=31%  Similarity=0.666  Sum_probs=33.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ...++|||+|||..+++++|+++|++||.|.++.++
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            367899999999999999999999999999999886

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

Probab=99.12  E-value=5.9e-11  Score=57.34  Aligned_cols=35  Identities=17%  Similarity=0.474  Sum_probs=33.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ++|||+|||..+++++|+++|++||.|.++.++.+
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

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.12  E-value=7e-11  Score=63.45  Aligned_cols=39  Identities=23%  Similarity=0.460  Sum_probs=36.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ...+|||+|||..+++++|+++|+.||.|.+++|+.|..
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            467899999999999999999999999999999998864

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.12  E-value=1.5e-10  Score=64.05  Aligned_cols=44  Identities=27%  Similarity=0.521  Sum_probs=40.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++. |+++|
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g  138 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG  138 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccce
Confidence            457999999999999999999999999999999999986 87776

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.11  E-value=8.3e-11  Score=65.03  Aligned_cols=56  Identities=20%  Similarity=0.255  Sum_probs=45.5

Q ss_pred             ceeecccCCCC-----CCCCeEEEcCCCCCC-cHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          3 PLDLIWNCTPL-----PPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~-----~~~~~l~v~~L~~~~-~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ++++.|+....     ...++|||+|||..+ ++++|+++|+.||.|.+++++.++.|+++|
T Consensus       166 ~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g  227 (284)
T 3smz_A          166 TLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKG  227 (284)
T ss_dssp             ECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEE
T ss_pred             EEEEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCccc
Confidence            34556655422     356789999999995 999999999999999999999998777765

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.11  E-value=1.9e-10  Score=61.85  Aligned_cols=38  Identities=26%  Similarity=0.393  Sum_probs=35.2

Q ss_pred             CCCeEEEcCCC-CCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~-~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++|||+||| ..+++++|+++|++||.|.+++++.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~   41 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK   41 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC
Confidence            56799999999 899999999999999999999998764

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

Probab=99.09  E-value=1.1e-11  Score=61.04  Aligned_cols=42  Identities=26%  Similarity=0.452  Sum_probs=34.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCe----EEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTI----EECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i----~~~~v~~d~~g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|+.||.|    ..+++.   .|+++|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g   68 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRG   68 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccce
Confidence            456899999999999999999999999998    444444   355555

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.08  E-value=2.7e-10  Score=55.79  Aligned_cols=34  Identities=29%  Similarity=0.733  Sum_probs=31.8

Q ss_pred             CCCeEEEcCCCCC-CcHHHHHHhhccCCCeEEEEE
Q psy10283         15 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        15 ~~~~l~v~~L~~~-~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ..++|||+|||.. +++++|+++|++||.|.++.+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i   60 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV   60 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE
Confidence            4589999999999 999999999999999999887

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

Probab=99.08  E-value=1.8e-10  Score=55.32  Aligned_cols=37  Identities=32%  Similarity=0.786  Sum_probs=32.9

Q ss_pred             CCCCCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEE
Q psy10283         13 LPPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        13 ~~~~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      .+..++|||+|||. .+++++|+++|++||.|.++.+.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~   44 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK   44 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe
Confidence            34678999999998 99999999999999999999874

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.07  E-value=1.5e-10  Score=57.11  Aligned_cols=36  Identities=11%  Similarity=0.303  Sum_probs=32.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      ..++|||+|||..+++++|+++|++||.|.++.++.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   44 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE   44 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC
Confidence            356899999999999999999999999999998764

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.06  E-value=4.2e-10  Score=62.13  Aligned_cols=45  Identities=20%  Similarity=0.474  Sum_probs=38.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHH----HhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~----~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      .....++|||+|||..+++++|+    ++|+.||.|.+++++.  .|++||
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g   53 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRG   53 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcce
Confidence            34568899999999999999976    8999999999998876  355665

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.06  E-value=2.5e-10  Score=54.88  Aligned_cols=37  Identities=14%  Similarity=0.159  Sum_probs=33.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ....|||+||++.+++++|+++|++||+|.++++...
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~   42 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN   42 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC
Confidence            4568999999999999999999999999999998763

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.06  E-value=2.5e-10  Score=54.60  Aligned_cols=37  Identities=24%  Similarity=0.580  Sum_probs=33.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHH----HhhccCCCeEEEEEE
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVL   49 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~----~~F~~~G~i~~~~v~   49 (59)
                      .+..++|||+|||..+++++|+    ++|++||.|.++.++
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~   45 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS   45 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEE
Confidence            4567899999999999999999    999999999999876

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.05  E-value=2.3e-10  Score=63.45  Aligned_cols=44  Identities=23%  Similarity=0.433  Sum_probs=39.6

Q ss_pred             CCCeEEEcCCCCC-CcHHHHHHhhccCCCeEEEEEEeCCC--CCCCC
Q psy10283         15 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPD--GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~-~~~~~l~~~F~~~G~i~~~~v~~d~~--g~~rG   58 (59)
                      ..++|||+|||.. +++++|+++|+.||.|..++++.+..  |+++|
T Consensus       209 ~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g  255 (292)
T 2ghp_A          209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC  255 (292)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCE
T ss_pred             CCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCce
Confidence            4578999999999 99999999999999999999999887  77776

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.04  E-value=4.2e-10  Score=54.30  Aligned_cols=43  Identities=28%  Similarity=0.444  Sum_probs=35.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|+.|+   ++.++.++. |+++|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g   55 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKG   55 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCc
Confidence            44678999999999999999999999774   677888876 77665

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.04  E-value=2.5e-10  Score=61.83  Aligned_cols=41  Identities=15%  Similarity=0.279  Sum_probs=37.4

Q ss_pred             CCCCCCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         12 PLPPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +.+..++|||+|||. .+++++|+++|+.||.|.+++++.++
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~   71 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK   71 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC
Confidence            445678999999999 99999999999999999999999875

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=3.2e-10  Score=54.47  Aligned_cols=36  Identities=14%  Similarity=0.352  Sum_probs=32.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..++|||+|||..+++++|+++|+.||.|. +.++.+
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~   53 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ   53 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC
Confidence            578999999999999999999999999996 666654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.03  E-value=8.7e-10  Score=53.04  Aligned_cols=36  Identities=25%  Similarity=0.367  Sum_probs=32.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccC--CCeEEEEEE
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPF--GTIEECTVL   49 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~--G~i~~~~v~   49 (59)
                      ...++|||+|||..+++++|+++|++|  |.|.++++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~   50 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI   50 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe
Confidence            357899999999999999999999999  999998765

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.03  E-value=5e-10  Score=57.04  Aligned_cols=37  Identities=24%  Similarity=0.350  Sum_probs=33.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..-+|||+||++.+++++|+++|++||.|.++.+..+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~   63 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK   63 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC
Confidence            4457899999999999999999999999999988764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.02  E-value=8.8e-10  Score=55.69  Aligned_cols=35  Identities=14%  Similarity=0.142  Sum_probs=31.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      ...|||+||++.+++++|+++|++||.|.++.+..
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~   59 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK   59 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            34578999999999999999999999999998865

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.02  E-value=4.1e-10  Score=59.28  Aligned_cols=39  Identities=23%  Similarity=0.322  Sum_probs=34.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      +....+|||+||++.+++++|+++|++||.|.++.+..+
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k   81 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK   81 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC
Confidence            334567999999999999999999999999999998654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.02  E-value=3.8e-10  Score=62.59  Aligned_cols=40  Identities=25%  Similarity=0.262  Sum_probs=36.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG   54 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g   54 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.+..+
T Consensus        40 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~   79 (292)
T 2ghp_A           40 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK   79 (292)
T ss_dssp             --CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC
Confidence            5789999999999999999999999999999999998754

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.00  E-value=7.9e-11  Score=60.01  Aligned_cols=35  Identities=26%  Similarity=0.488  Sum_probs=30.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEE
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC   46 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~   46 (59)
                      +....++|||+|||+.+++++|+++|+.||.|..+
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~   75 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSE   75 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccc
Confidence            34567899999999999999999999999998764

>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=98.99  E-value=2.9e-10  Score=56.83  Aligned_cols=38  Identities=13%  Similarity=0.235  Sum_probs=33.3

Q ss_pred             CCCCeEEE--cCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         14 PPDKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v--~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...++|||  |||+..+++++|+++|++||.|.++.++.+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~   62 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN   62 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC
Confidence            35678999  779999999999999999999999877643

>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=98.96  E-value=4.7e-10  Score=53.39  Aligned_cols=37  Identities=24%  Similarity=0.361  Sum_probs=31.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCC-eEEEEE
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTV   48 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~-i~~~~v   48 (59)
                      .....++|||+|||..+++++|+++|++||. |..+.+
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~   41 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL   41 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE
Confidence            3456789999999999999999999999999 555544

>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=98.96  E-value=3.3e-10  Score=60.95  Aligned_cols=37  Identities=16%  Similarity=0.193  Sum_probs=33.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCe--EEEEEEeCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTI--EECTVLKGP   52 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i--~~~~v~~d~   52 (59)
                      .++|||+|||+.+++++|+++|++||.|  .+++++.+.
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~  161 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK  161 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC
Confidence            4579999999999999999999999999  888888775

>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=98.95  E-value=2.5e-09  Score=55.35  Aligned_cols=52  Identities=23%  Similarity=0.226  Sum_probs=40.1

Q ss_pred             ceeecccCCCC----CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          3 PLDLIWNCTPL----PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         3 ~~~~~~~~~~~----~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ++++.|+....    ...++|||+|||..+++++|+++|++||.|..+    ...|+++|
T Consensus        82 ~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g  137 (175)
T 1fje_B           82 EIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKG  137 (175)
T ss_dssp             EEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCS
T ss_pred             EEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCce
Confidence            45666666532    246789999999999999999999999988765    33377776

>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=98.94  E-value=7.1e-10  Score=52.04  Aligned_cols=38  Identities=16%  Similarity=0.342  Sum_probs=34.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccC----C-------CeEEEEEEeC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPF----G-------TIEECTVLKG   51 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~----G-------~i~~~~v~~d   51 (59)
                      ...++|||+|||..+++++|+++|++|    |       .|.++++..+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~   52 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD   52 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC
Confidence            356899999999999999999999999    8       9999988765

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.91  E-value=2.1e-10  Score=54.84  Aligned_cols=33  Identities=21%  Similarity=0.282  Sum_probs=29.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEE
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC   46 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~   46 (59)
                      ...++|||+|||..+++++|+++|+.||.|..+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~   46 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV   46 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe
Confidence            356899999999999999999999999988765

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.90  E-value=1.3e-09  Score=57.49  Aligned_cols=37  Identities=16%  Similarity=0.357  Sum_probs=34.7

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         16 DKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        16 ~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .++|||+|||. .+++++|+++|+.||.|.+++++.++
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~   40 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK   40 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC
Confidence            57999999999 99999999999999999999998875

>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=98.89  E-value=2.2e-09  Score=59.12  Aligned_cols=38  Identities=26%  Similarity=0.529  Sum_probs=34.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++|||+|||..+++++|+++|+.||.|.++.+..++
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            45789999999999999999999999999999987653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.85  E-value=3e-09  Score=58.82  Aligned_cols=37  Identities=24%  Similarity=0.482  Sum_probs=33.9

Q ss_pred             CCCeEEEcCCCCCC---------cHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQ---------NEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~---------~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..++||||||+..+         ++++|+++|++||.|.+++++.+
T Consensus       133 ~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~  178 (240)
T 3u1l_A          133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES  178 (240)
T ss_dssp             CCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG
T ss_pred             CCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC
Confidence            56899999999998         79999999999999999998864

>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=98.84  E-value=8.5e-09  Score=56.90  Aligned_cols=38  Identities=26%  Similarity=0.471  Sum_probs=35.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~  243 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR  243 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC
Confidence            46789999999999999999999999999999998765

>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=98.83  E-value=5.2e-09  Score=49.40  Aligned_cols=34  Identities=18%  Similarity=0.372  Sum_probs=31.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ..++|||+|||..+++++|+++|++| .|.++++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~   37 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD   37 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe
Confidence            46789999999999999999999999 99998874

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.82  E-value=2.2e-08  Score=47.94  Aligned_cols=34  Identities=24%  Similarity=0.331  Sum_probs=30.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ...++|||+|+  .+++++|+++|++||.|.++.+.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~   46 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD   46 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec
Confidence            35789999995  89999999999999999999885

>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=98.74  E-value=3.2e-10  Score=58.77  Aligned_cols=46  Identities=13%  Similarity=0.249  Sum_probs=35.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+...++|||+|||..+++++|+++|+.||.+.. .++.+.. |+++|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g   55 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRK   55 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCcccc
Confidence            4456889999999999999999999999987666 2333333 66665

>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=98.73  E-value=5.2e-08  Score=52.71  Aligned_cols=36  Identities=14%  Similarity=0.373  Sum_probs=33.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCC-CeEEEEEEeC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKG   51 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G-~i~~~~v~~d   51 (59)
                      .++|||+|||..+++++|+++|++|| .|.+++++.+
T Consensus       151 ~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~  187 (229)
T 2adc_A          151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  187 (229)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC
Confidence            57899999999999999999999999 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=98.73  E-value=2.9e-08  Score=52.29  Aligned_cols=37  Identities=16%  Similarity=0.432  Sum_probs=33.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCC-CeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G-~i~~~~v~~d   51 (59)
                      ..++|||+|||..+++++|+++|+.|| .|.+++++.+
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence            367899999999999999999999999 9999998664

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.66  E-value=5e-08  Score=47.39  Aligned_cols=31  Identities=16%  Similarity=0.278  Sum_probs=26.4

Q ss_pred             CCe-EEEcCCCCCCcHHH----HHHhhccC-CCeEEE
Q psy10283         16 DKK-LFVGMLSKQQNEDD----VRKIFAPF-GTIEEC   46 (59)
Q Consensus        16 ~~~-l~v~~L~~~~~~~~----l~~~F~~~-G~i~~~   46 (59)
                      ..+ |||+|||+.+++++    |+++|++| |+|.++
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V   44 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI   44 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE
Confidence            444 99999999999887    55899999 599886

>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=98.64  E-value=2.8e-08  Score=57.34  Aligned_cols=38  Identities=11%  Similarity=0.171  Sum_probs=32.6

Q ss_pred             CCCCCeEEEcC--CCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         13 LPPDKKLFVGM--LSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        13 ~~~~~~l~v~~--L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      .....+|||||  |++.+++++|+++|++||+|.++.+..
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~   54 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP   54 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC
Confidence            34678999999  588999999999999999999876643

>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=98.58  E-value=5.1e-08  Score=50.12  Aligned_cols=37  Identities=16%  Similarity=0.365  Sum_probs=32.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccC----C-------CeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPF----G-------TIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~----G-------~i~~~~v~~d   51 (59)
                      ..++|||+|||..+++++|+++|++|    |       .|.++.+..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~   50 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD   50 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC
Confidence            35799999999999999999999999    7       7787776544

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=1.2e-07  Score=47.77  Aligned_cols=40  Identities=15%  Similarity=0.165  Sum_probs=36.3

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         14 PPDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        14 ~~~~~l~v~~L~~~-~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ..++-|||+||+.. ++.++|+++|+.||.|..|.+..+..
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~   56 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK   56 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC
Confidence            46788999999999 99999999999999999999887764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.55  E-value=2.4e-07  Score=45.31  Aligned_cols=44  Identities=14%  Similarity=0.375  Sum_probs=35.5

Q ss_pred             CCCeEEEcCCCC-----CCcHHHHHHhhccCCCeEEEEEEeCCC--CCCCC
Q psy10283         15 PDKKLFVGMLSK-----QQNEDDVRKIFAPFGTIEECTVLKGPD--GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~-----~~~~~~l~~~F~~~G~i~~~~v~~d~~--g~~rG   58 (59)
                      ..+.|++.|+..     .-.+++|++.|++||.|.++.|+.++.  ++++|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G   57 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAV   57 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSE
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcE
Confidence            467899999862     236789999999999999999999865  56776

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.49  E-value=1.8e-07  Score=49.01  Aligned_cols=36  Identities=17%  Similarity=0.349  Sum_probs=30.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccC----C-------CeEEEEEEe
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPF----G-------TIEECTVLK   50 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~----G-------~i~~~~v~~   50 (59)
                      ..++|||+|||..+++++|+++|+.|    |       .|.++.+..
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~   49 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ   49 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecC
Confidence            46899999999999999999999999    5       666666543

>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=98.18  E-value=1.2e-07  Score=46.32  Aligned_cols=38  Identities=13%  Similarity=0.232  Sum_probs=30.4

Q ss_pred             EcCCCCCCcHHHHHHhh------------ccCCCeEEEEEEeCCCCCCCC
Q psy10283         21 VGMLSKQQNEDDVRKIF------------APFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        21 v~~L~~~~~~~~l~~~F------------~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +.+|+..+++++|++.|            ++||.|.++.++.+..|+++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G   69 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG   69 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccE
Confidence            56677777887777666            999999999999887677776

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.16  E-value=1.6e-05  Score=38.56  Aligned_cols=24  Identities=8%  Similarity=0.243  Sum_probs=22.3

Q ss_pred             CCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         26 KQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        26 ~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ..+++++|+++|++||.|.++.++
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~   50 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS   50 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc
Confidence            568999999999999999999987

>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=98.09  E-value=1.7e-05  Score=38.74  Aligned_cols=39  Identities=13%  Similarity=0.279  Sum_probs=30.5

Q ss_pred             CCCCCeEEEcCCCCCCc-----------HHHHHHhhccCCCeEEEEEEeCC
Q psy10283         13 LPPDKKLFVGMLSKQQN-----------EDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~-----------~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +...+.|++.||.....           +++|+++|++||.|.++.+ .|+
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~   61 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR   61 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC
Confidence            44678899999954432           5789999999999999955 554

>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=97.60  E-value=5.4e-05  Score=36.81  Aligned_cols=44  Identities=18%  Similarity=0.314  Sum_probs=32.1

Q ss_pred             CCCeEEEcCC--CCCC--------cHHHHHHhhccCCCeEEEEEEeCCCC---CCCC
Q psy10283         15 PDKKLFVGML--SKQQ--------NEDDVRKIFAPFGTIEECTVLKGPDG---TSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L--~~~~--------~~~~l~~~F~~~G~i~~~~v~~d~~g---~~rG   58 (59)
                      ..+-|.+.|+  +...        .+++|++.|++||.|.++.|++++.+   +++|
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G   60 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCG   60 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTT
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcE
Confidence            3456777886  2233        23689999999999999999988762   4555

>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=97.25  E-value=0.0009  Score=33.19  Aligned_cols=39  Identities=10%  Similarity=0.261  Sum_probs=30.7

Q ss_pred             CCCeEEEcCCCC--C---CcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGMLSK--Q---QNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L~~--~---~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ..+.|++.|+-.  .   --+++|++.|++||.|.++.|+.++.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~   62 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQ   62 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCC
Confidence            467789999732  1   23578999999999999999998754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.57  E-value=0.0047  Score=29.61  Aligned_cols=39  Identities=18%  Similarity=0.360  Sum_probs=28.0

Q ss_pred             CCCCeEEEcCCCC----C-CcH---HHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSK----Q-QNE---DDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~----~-~~~---~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +...+++|...+.    . ..+   .+|.+.|++||.|..++++.|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~   51 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK   51 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC
Confidence            3456777766551    2 232   4688999999999999988764

>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=96.55  E-value=0.0018  Score=31.89  Aligned_cols=39  Identities=18%  Similarity=0.101  Sum_probs=27.1

Q ss_pred             CCCCeEEEcCCCCCC----------cHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSKQQ----------NEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~----------~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ...+-|.+.|+-..-          -+++|++.|++||.|.++.+.++.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~   53 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS   53 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC
Confidence            345567777762221          124788999999999999887664

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.91  E-value=0.021  Score=27.76  Aligned_cols=35  Identities=17%  Similarity=0.410  Sum_probs=25.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...||.-..|......+|..+|++||.+ .++++-|
T Consensus        15 r~HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidD   49 (100)
T 1whv_A           15 RDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD   49 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET
T ss_pred             CCeEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcC
Confidence            3344444999999999999999999853 3444433

>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=95.24  E-value=0.011  Score=31.55  Aligned_cols=25  Identities=16%  Similarity=0.352  Sum_probs=21.1

Q ss_pred             cHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         29 NEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        29 ~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      .++++++.|++||.|.++.|..+..
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~  166 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQ  166 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEEC
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCC
Confidence            4578999999999999999986644

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=95.08  E-value=0.028  Score=28.01  Aligned_cols=44  Identities=7%  Similarity=-0.002  Sum_probs=36.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHhhccC-----CCeEEEEEEeCCC
Q psy10283         10 CTPLPPDKKLFVGMLSKQQNEDDVRKIFAPF-----GTIEECTVLKGPD   53 (59)
Q Consensus        10 ~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~-----G~i~~~~v~~d~~   53 (59)
                      ..+.+..+.+-+-+||..++...++.+.+++     |.+.++.+..|-.
T Consensus        15 ~~~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~   63 (117)
T 2l9w_A           15 RNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN   63 (117)
T ss_dssp             CCTTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT
T ss_pred             cCCccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC
Confidence            3344567889999999999999999999999     9999988776643

>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=94.90  E-value=0.069  Score=26.01  Aligned_cols=33  Identities=15%  Similarity=0.365  Sum_probs=24.9

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .+|.-..|......+|..+|++||. ..++++-|
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fgg-v~I~WidD   39 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDD   39 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEE-EEEEEEET
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCC-EEEEEEcC
Confidence            3444499999999999999999994 44555544

>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=94.63  E-value=0.012  Score=28.38  Aligned_cols=40  Identities=23%  Similarity=0.350  Sum_probs=29.6

Q ss_pred             CCCCCeEEEcCCCCC------CcH---HHHHHhhccCCCeEEEEEEeCC
Q psy10283         13 LPPDKKLFVGMLSKQ------QNE---DDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~------~~~---~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .+...+++|..++..      ..+   .+|.+.|++||.|..+++..|+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~   60 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ   60 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc
Confidence            345778888877632      232   3588899999999999988764

>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=93.61  E-value=0.27  Score=23.36  Aligned_cols=32  Identities=9%  Similarity=0.228  Sum_probs=26.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      .+|-|.+||+..+++++.+.++....+.-...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~f   33 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEF   33 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEE
Confidence            47889999999999999999998876654443

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.58  E-value=0.3  Score=23.87  Aligned_cols=35  Identities=11%  Similarity=0.022  Sum_probs=29.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhcc-C----CCeEEEEE
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAP-F----GTIEECTV   48 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~-~----G~i~~~~v   48 (59)
                      ...++|.|.|||..+.++.|.-.|++ -    |+|.+++.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~   45 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQR   45 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEE
Confidence            45788999999999999999999987 2    67877754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.33  E-value=0.071  Score=32.15  Aligned_cols=33  Identities=15%  Similarity=0.360  Sum_probs=25.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      .+.|||. .+..+++.+|.+.|++||.|.++..-
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~   85 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFY   85 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEE
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEE
Confidence            4579997 69999999999999999999987543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=89.70  E-value=0.27  Score=23.70  Aligned_cols=28  Identities=7%  Similarity=0.227  Sum_probs=22.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGT   42 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~   42 (59)
                      ..-+|-|..||+..|++++.+.++.+-.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~   35 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPA   35 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSS
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCc
Confidence            3458999999999999998887776544

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=83.85  E-value=1.8  Score=21.59  Aligned_cols=33  Identities=18%  Similarity=0.179  Sum_probs=25.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ..+.|.|-+-|... ...+...|++||.|.+...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~   55 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM   55 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc
Confidence            46788888888775 4456778999999998764

---

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	59
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-06
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-04
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-04
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	8e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	8e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	9e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 0.001
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.001
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.001
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	0.001
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	0.002
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.003
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	0.003
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	0.003

>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 = 40.3 bits (94), Expect = 5e-07
 Identities = 11/44 (25%), Positives = 22/44 (50%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
              K+ V  +  Q N+ ++R++F+ FG ++   + K   GT  
Sbjct: 6  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGA 49

>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 = 40.2 bits (94), Expect = 5e-07
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 12 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
          P   + ++F+G L+     + DV  IF+ +G I  C+V KG
Sbjct: 11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG 51

>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 = 40.0 bits (93), Expect = 8e-07
 Identities = 10/37 (27%), Positives = 19/37 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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 = 40.4 bits (93), Expect = 1e-06
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
           +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 = 3e-06
 Identities = 10/33 (30%), Positives = 15/33 (45%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
           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 = 3e-06
 Identities = 11/33 (33%), Positives = 20/33 (60%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          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 = 4e-06
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          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 = 6e-06
 Identities = 7/31 (22%), Positives = 13/31 (41%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          +  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 = 36.9 bits (85), Expect = 1e-05
 Identities = 8/31 (25%), Positives = 16/31 (51%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          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 = 1e-05
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
           P+  L V  LS    E D+R++F+ +G I + 
Sbjct: 7  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADV 39

>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 = 2e-05
 Identities = 12/29 (41%), Positives = 20/29 (68%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          K+F+G LS Q  ++ +R+ F  FG ++EC
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKEC 30

>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 = 35.8 bits (82), Expect = 2e-05
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
          LF+  L+    E+ ++ +F+  G I+ CT+ K  +      
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL 41

>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 = 3e-05
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          K+FVG LS    E+ +R+ F  FG +E  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESI 29

>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 = 35.5 bits (81), Expect = 4e-05
 Identities = 7/42 (16%), Positives = 16/42 (38%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
          ++L+VG +     E+ +   F     +   T   G    + +
Sbjct: 2  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ 43

>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 = 35.4 bits (81), Expect = 4e-05
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
            D  ++VG L ++ +E  + ++F   G +   
Sbjct: 7  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNT 39

>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 = 34.7 bits (79), Expect = 6e-05
 Identities = 9/39 (23%), Positives = 17/39 (43%)

Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
          +F+G L  + +E  +   F+ FG I +   +     T  
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGN 39

>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 = 34.5 bits (79), Expect = 1e-04
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          L     L+VG LS    E+ + ++F+  G I++ 
Sbjct: 4  LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI 37

>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 = 34.3 bits (78), Expect = 1e-04
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
          KL++G LS     DD+R++F          VL 
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 35

>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 = 33.9 bits (77), Expect = 2e-04
 Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
           +KLF+G LS +  ++ +R  F  +GT+ +C V++ P+   S+
Sbjct: 6  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSR 48

>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 = 33.6 bits (76), Expect = 2e-04
 Identities = 2/31 (6%), Positives = 10/31 (32%)

Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          +  L++        + ++R +      +   
Sbjct: 1  ECTLWMTNFPPSYTQRNIRDLLQDINVVALS 31

>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 = 33.8 bits (77), Expect = 3e-04
 Identities = 7/35 (20%), Positives = 17/35 (48%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          P   ++ L++  L  +   +++  IF  +G I + 
Sbjct: 3  PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI 37

>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 = 33.1 bits (75), Expect = 3e-04
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
             + L+VG L+++ ++  +   F PFG I + 
Sbjct: 3  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 35

>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 = 33.0 bits (75), Expect = 3e-04
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          +LFVG L     E+++RK+F  +G   E 
Sbjct: 10 RLFVGNLPPDITEEEMRKLFEKYGKAGEV 38

>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 = 33.5 bits (76), Expect = 3e-04
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
             K+L V  +  +  + D+R++F  FG I + 
Sbjct: 9  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV 41

>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 = 33.2 bits (75), Expect = 3e-04
 Identities = 7/39 (17%), Positives = 14/39 (35%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
            +  ++V  L+     DD+   F   G ++       P
Sbjct: 6  SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQP 44

>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 = 4e-04
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
          K+F+G LS    + D++  F+ FG + +CT+   P 
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI 36

>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 = 32.7 bits (74), Expect = 5e-04
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
             + L+VG LS+   E  + ++F+  G  + C
Sbjct: 6  GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSC 38

>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 = 32.4 bits (73), Expect = 5e-04
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          K+FVG LS     +DV+  F  FG +++ 
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDA 29

>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 = 32.3 bits (73), Expect = 6e-04
 Identities = 10/37 (27%), Positives = 17/37 (45%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
           +F+  L K  +   +   F+ FG I  C V+   +G
Sbjct: 10 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG 46

>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 = 32.4 bits (73), Expect = 6e-04
 Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 7/38 (18%)

Query: 9  NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          NC       +LF+G + K +  +++ +  A        
Sbjct: 1  NC-------RLFIGGIPKMKKREEILEEIAKVTEGVLD 31

>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 = 32.5 bits (73), Expect = 6e-04
 Identities = 9/37 (24%), Positives = 16/37 (43%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
             F G L  Q   +D+  +F+  G I+    ++G  
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK 48

>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 = 32.3 bits (73), Expect = 7e-04
 Identities = 8/33 (24%), Positives = 15/33 (45%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
            D +++VG L       D+  +F  +G I + 
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI 44

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.0 bits (72), Expect = 8e-04
 Identities = 7/34 (20%), Positives = 17/34 (50%)

Query: 13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
           PP   L +  +    +E+D++ +F+  G + + 
Sbjct: 7  FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG 40

>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 = 32.3 bits (73), Expect = 8e-04
 Identities = 5/30 (16%), Positives = 13/30 (43%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          + +F   L+ +    D+   F+  G + + 
Sbjct: 19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDV 48

>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 = 8e-04
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 9  NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          +  P  P+K L++  LS +  E D+  +FA F   +  
Sbjct: 11 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGP 48

>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 = 32.0 bits (72), Expect = 9e-04
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
           P  +L+VG L    +   + + F  FG+I   
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI 47

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.9 bits (72), Expect = 0.001
 Identities = 5/41 (12%), Positives = 13/41 (31%)

Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
            + +     +  E+   ++   +G +EE  V         
Sbjct: 28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLV 68

>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 = 31.6 bits (71), Expect = 0.001
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
          P    LF+  L ++  + D+ ++F PFG +   
Sbjct: 16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA 48

>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 = 31.6 bits (71), Expect = 0.001
 Identities = 12/40 (30%), Positives = 23/40 (57%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
            +KLF+G LS +  E+ +R  +  +G + +C V++ P  
Sbjct: 19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPAS 58

>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 = 31.6 bits (71), Expect = 0.001
 Identities = 8/41 (19%), Positives = 15/41 (36%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT 55
            + L    LS    ED+++++F     I   +      G 
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGI 55

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.2 bits (70), Expect = 0.002
 Identities = 7/37 (18%), Positives = 12/37 (32%)

Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
          P  P    F+G L     E+ +++ F           
Sbjct: 11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLP 47

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 30.8 bits (69), Expect = 0.003
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
              +LFV  LS   +E+D+ K+F+ +G + E 
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSEL 38

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.4 bits (68), Expect = 0.003
 Identities = 8/33 (24%), Positives = 17/33 (51%)

Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
               +FVG  +    ED++R+ F+ +G + + 
Sbjct: 3  SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDV 35

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.5 bits (68), Expect = 0.003
 Identities = 9/29 (31%), Positives = 14/29 (48%)

Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
           L V  L +   +++ R +F   G IE C
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESC 32

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.3 bits (68), Expect = 0.003
 Identities = 8/32 (25%), Positives = 14/32 (43%)

Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
              L V  L  +  E D+++ F+ FG +   
Sbjct: 7  KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMV 38

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	59
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.63
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.61
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.61
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.61
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.6
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.59
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.58
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.58
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.57
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.57
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.56
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.56
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.56
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.55
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.55
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.55
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.54
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.53
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.53
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.53
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.52
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.52
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.52
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.51
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.5
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.49
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.48
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.46
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.46
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.46
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.45
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.45
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.42
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.41
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.39
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.39
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.37
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.36
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.36
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.35
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.35
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.33
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.33
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.32
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.31
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.31
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.29
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.27
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.27
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.26
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.26
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.26
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.25
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.23
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.21
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.2
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.19
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.19
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.18
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.17
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.17
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.16
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.16
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.15
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.13
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.13
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.12
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.11
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.11
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.05
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.03
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.01
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.0
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.92
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.9
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.87
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.84
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.83
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.54
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	98.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.27
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	97.09
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	94.66
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.49
d1qyra_	252	High level kasugamycin resistance protein KsgA {Es	85.86

>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=99.65  E-value=1.6e-16  Score=75.44  Aligned_cols=46  Identities=28%  Similarity=0.385  Sum_probs=42.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .....+|||+|||+++++++|+++|++||.|.++++++|+. |++||
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG   51 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG   51 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEE
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCC
Confidence            34567899999999999999999999999999999999988 99887

>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=99.65  E-value=8.4e-17  Score=74.56  Aligned_cols=42  Identities=36%  Similarity=0.699  Sum_probs=40.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      |+|||+|||+++++++|+++|++||.|.++++++|+. |++||
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG   43 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG   43 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccc
Confidence            6899999999999999999999999999999999998 99998

>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=99.63  E-value=1.2e-16  Score=73.71  Aligned_cols=41  Identities=29%  Similarity=0.532  Sum_probs=39.5

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +|||||||+++++++|+++|++||.|.+++++.|+. |++||
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG   42 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG   42 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccccccccccccccc
Confidence            699999999999999999999999999999999988 99988

>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=99.63  E-value=1.7e-16  Score=74.52  Aligned_cols=45  Identities=31%  Similarity=0.680  Sum_probs=41.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||+.+++++|+++|++||.|.++++++|+. |++||
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG   49 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG   49 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCccc
Confidence            4567999999999999999999999999999999999998 88887

>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=99.61  E-value=1.2e-15  Score=73.79  Aligned_cols=45  Identities=36%  Similarity=0.586  Sum_probs=41.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||+.+++++|+++|+.||.|.+++++.|+. |++||
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg   53 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG   53 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCS
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCC
Confidence            3457899999999999999999999999999999999988 99987

>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=99.61  E-value=5e-16  Score=72.91  Aligned_cols=44  Identities=25%  Similarity=0.499  Sum_probs=40.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+++|||+|||+.+++++|+++|++||+|.+++++.|+. |++||
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg   49 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG   49 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCC
Confidence            467899999999999999999999999999999999987 88776

>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=99.61  E-value=8.1e-16  Score=72.20  Aligned_cols=42  Identities=33%  Similarity=0.654  Sum_probs=40.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+|||+|||..+++++|+++|++||+|.++++++|+. |++||
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg   44 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG   44 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccce
Confidence            5899999999999999999999999999999999988 99887

>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=99.60  E-value=5.7e-16  Score=71.28  Aligned_cols=41  Identities=34%  Similarity=0.690  Sum_probs=39.4

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +|||+|||+++++++|+++|++||+|.+++++.|+. |+++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg   42 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRG   42 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCS
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCc
Confidence            699999999999999999999999999999999988 99887

>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=99.59  E-value=9.9e-16  Score=71.48  Aligned_cols=45  Identities=27%  Similarity=0.392  Sum_probs=41.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|++||.|.+++++.|+. |+++|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   52 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG   52 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Confidence            4567899999999999999999999999999999999988 88776

>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=99.58  E-value=2.3e-15  Score=70.48  Aligned_cols=44  Identities=25%  Similarity=0.527  Sum_probs=41.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||..+++++|+++|++||+|.++++++|+. |++||
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g   49 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG   49 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCce
Confidence            567899999999999999999999999999999999988 88876

>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=99.58  E-value=2.9e-15  Score=71.28  Aligned_cols=45  Identities=20%  Similarity=0.324  Sum_probs=41.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +..++|||+|||..+++++|+++|++||.|.+++++.|+. |++||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg   52 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG   52 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeeccccccccc
Confidence            4567999999999999999999999999999999999988 88887

>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=99.57  E-value=1.4e-15  Score=71.79  Aligned_cols=44  Identities=20%  Similarity=0.453  Sum_probs=41.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||+.+++++|+++|++||+|.+++++.|+. |++||
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg   48 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG   48 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccc
Confidence            457899999999999999999999999999999999998 99987

>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=99.57  E-value=3.3e-15  Score=71.63  Aligned_cols=46  Identities=26%  Similarity=0.379  Sum_probs=42.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||+.+++++|+++|++||.|.+++++.|+. |+++|
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g   51 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG   51 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCS
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCc
Confidence            34577899999999999999999999999999999999988 98887

>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=99.57  E-value=1.3e-15  Score=70.81  Aligned_cols=43  Identities=21%  Similarity=0.513  Sum_probs=40.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +++|||+|||..+++++|+++|++||.|.++++++|+. |+++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g   45 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG   45 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccc
Confidence            56899999999999999999999999999999999887 88887

>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=99.56  E-value=4.9e-15  Score=71.47  Aligned_cols=44  Identities=16%  Similarity=0.369  Sum_probs=41.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKER   59 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG~   59 (59)
                      .++|||+|||+.+++++|+++|+.||.|.++++++|.. |++||.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~   62 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI   62 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccce
Confidence            46799999999999999999999999999999999988 999984

>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=99.56  E-value=3.9e-15  Score=69.14  Aligned_cols=43  Identities=26%  Similarity=0.571  Sum_probs=39.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|++||.|.+++++.|.. |+++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g   45 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG   45 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCcee
Confidence            45799999999999999999999999999999999887 77776

>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=99.56  E-value=3.4e-15  Score=71.02  Aligned_cols=45  Identities=22%  Similarity=0.255  Sum_probs=41.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..+++|||+|||..+++++|+++|++||.|.++.++.++. |++||
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg   50 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG   50 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccc
Confidence            3568999999999999999999999999999999999988 87776

>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=99.55  E-value=4e-15  Score=68.74  Aligned_cols=43  Identities=28%  Similarity=0.570  Sum_probs=40.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||||||+++++++|+++|++||.+..+.+..++. ++++|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g   45 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG   45 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCccccc
Confidence            47899999999999999999999999999999999987 77776

>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=99.55  E-value=3.3e-15  Score=69.34  Aligned_cols=41  Identities=27%  Similarity=0.290  Sum_probs=38.9

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .|||||||+.+++++|+++|++||+|.++++++|+. |+++|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g   43 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG   43 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCC
Confidence            599999999999999999999999999999999988 88876

>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=99.55  E-value=5.8e-15  Score=71.46  Aligned_cols=43  Identities=30%  Similarity=0.685  Sum_probs=40.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||||||+++++++|+++|++||.|.++.|+.|+. +++||
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg   63 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG   63 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccC
Confidence            46899999999999999999999999999999999988 78887

>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=99.54  E-value=7.3e-15  Score=69.42  Aligned_cols=45  Identities=31%  Similarity=0.516  Sum_probs=41.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||..+++++|+++|++||.|.+++++.|+. |++||
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg   51 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG   51 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccccccccccccccccc
Confidence            4567899999999999999999999999999999999987 88876

>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=99.53  E-value=1.3e-14  Score=69.09  Aligned_cols=45  Identities=22%  Similarity=0.474  Sum_probs=41.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC--CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD--GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~--g~~rG   58 (59)
                      ....+|||+|||..+++++|+++|++||.|.+++++.+..  |++||
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg   52 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG   52 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCccc
Confidence            4567899999999999999999999999999999998865  88887

>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=99.53  E-value=5.4e-15  Score=68.33  Aligned_cols=41  Identities=32%  Similarity=0.507  Sum_probs=39.2

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +|||+|||+.+++++|+++|++||.|.++++..++.|+++|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g   42 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG   42 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccce
Confidence            79999999999999999999999999999999998888887

>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=99.53  E-value=6.9e-15  Score=69.38  Aligned_cols=45  Identities=36%  Similarity=0.605  Sum_probs=41.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+.. |+++|
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g   48 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG   48 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccc
Confidence            3567899999999999999999999999999999998887 88887

>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=99.52  E-value=1.2e-14  Score=68.47  Aligned_cols=44  Identities=25%  Similarity=0.413  Sum_probs=40.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ++..|||+|||..+++++|+++|++||.|.+++++.|+. |++||
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g   50 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG   50 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccccccccccc
Confidence            567899999999999999999999999999999999987 88876

>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=99.52  E-value=2.1e-14  Score=69.03  Aligned_cols=51  Identities=20%  Similarity=0.431  Sum_probs=42.8

Q ss_pred             ccCCCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283          8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus         8 ~~~~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ++.......++|||+|||.++++++|+++|++||.|..+.+..+..++++|
T Consensus        10 ~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g   60 (101)
T d1x5oa1          10 MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG   60 (101)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEE
T ss_pred             hhccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccccccccc
Confidence            333344466899999999999999999999999999999999886676665

>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=99.52  E-value=9.9e-15  Score=70.37  Aligned_cols=45  Identities=27%  Similarity=0.511  Sum_probs=41.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +.+++|||+|||+.+++++|+++|+.||.+.+++++.++. |++||
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG   61 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC   61 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCcc
Confidence            3567899999999999999999999999999999999988 88876

>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=99.51  E-value=6.6e-15  Score=74.06  Aligned_cols=44  Identities=20%  Similarity=0.427  Sum_probs=40.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||.++++++|+++|+.||.|.+++++.|+. |++||
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg   85 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG   85 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccc
Confidence            346899999999999999999999999999999999987 88776

>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=99.50  E-value=2e-14  Score=67.35  Aligned_cols=43  Identities=9%  Similarity=0.225  Sum_probs=39.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      .++|||+|||..+++++|+++|+.||.|.++++..+..|++||
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG   48 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG   48 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcce
Confidence            5789999999999999999999999999999999887788776

>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=99.49  E-value=3.5e-14  Score=67.60  Aligned_cols=45  Identities=27%  Similarity=0.457  Sum_probs=41.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ...++|||+|||+.+++++|+++|++||.+.++.++.+.. ++++|
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g   51 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG   51 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCS
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccc
Confidence            4578999999999999999999999999999999999887 77777

>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=99.48  E-value=8.2e-15  Score=70.72  Aligned_cols=43  Identities=21%  Similarity=0.485  Sum_probs=40.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||..+++++|+++|++||.|.+++++.++. |++||
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g   51 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG   51 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCC
Confidence            46799999999999999999999999999999999987 88776

>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=99.46  E-value=8.6e-14  Score=63.18  Aligned_cols=40  Identities=20%  Similarity=0.405  Sum_probs=38.1

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        19 l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      |||+|||.++++++|+++|++||.|.++++..++. ++++|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g   41 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG   41 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccc
Confidence            79999999999999999999999999999999988 88887

>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=99.46  E-value=1.2e-13  Score=67.36  Aligned_cols=45  Identities=18%  Similarity=0.378  Sum_probs=38.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      |+..+++|||+|||..+++++|+++|++||.|.++++..+  +++||
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG   47 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRG   47 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTT
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCC
Confidence            3456789999999999999999999999999999998765  44555

>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=99.46  E-value=2.4e-14  Score=65.38  Aligned_cols=41  Identities=27%  Similarity=0.556  Sum_probs=38.2

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      +|||||||.++++++|+++|++||.+..+.++.++. |+++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~   42 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG   42 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCc
Confidence            699999999999999999999999999999999887 77776

>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=99.45  E-value=3e-13  Score=64.08  Aligned_cols=45  Identities=27%  Similarity=0.472  Sum_probs=39.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ....++|||+|||+.+++++|+++|++||.|.+++++.++.+ ++|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg   52 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKG   52 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-Ccc
Confidence            345778999999999999999999999999999999998753 344

>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=99.45  E-value=2.7e-14  Score=66.15  Aligned_cols=43  Identities=12%  Similarity=0.243  Sum_probs=34.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .++|||+|||.++++++|+++|++||.|..+.++.+.. |+++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g   44 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR   44 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccc
Confidence            46899999999999999999999999999888887776 88887

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=6.8e-14  Score=66.63  Aligned_cols=43  Identities=14%  Similarity=0.305  Sum_probs=38.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCC-eEEEEEEeCCC--CCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVLKGPD--GTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~-i~~~~v~~d~~--g~~rG   58 (59)
                      +++|||||||..+++++|+++|+.||. |.++.++.|..  |++||
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg   46 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRG   46 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCC
Confidence            478999999999999999999999996 99999998865  77877

>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=99.41  E-value=1.9e-13  Score=64.40  Aligned_cols=40  Identities=23%  Similarity=0.484  Sum_probs=37.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ...++|||+|||..+++++|+++|++||.|.+++++.|..
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~   45 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT   45 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccC
Confidence            3467999999999999999999999999999999999876

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=1.1e-13  Score=64.27  Aligned_cols=40  Identities=33%  Similarity=0.670  Sum_probs=36.5

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeEEE-EEEeCCC-CCCCC
Q psy10283         19 LFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD-GTSKE   58 (59)
Q Consensus        19 l~v~~L~~~~~~~~l~~~F~~~G~i~~~-~v~~d~~-g~~rG   58 (59)
                      |||+|||.++++++|+++|++||.|.++ +++.|+. |+++|
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g   42 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKG   42 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCS
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCc
Confidence            7999999999999999999999999764 7888888 88887

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.39  E-value=9.3e-14  Score=65.08  Aligned_cols=44  Identities=23%  Similarity=0.410  Sum_probs=36.2

Q ss_pred             CCCeEEEcCCCCCCc-HHHHHHhhccCCCeEEEEEEeCC-C-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQN-EDDVRKIFAPFGTIEECTVLKGP-D-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~-~~~l~~~F~~~G~i~~~~v~~d~-~-g~~rG   58 (59)
                      +.++|||+|||++++ ++.|+++|++||.|.++++..+. . |+++|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg   49 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC   49 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccce
Confidence            468999999999875 56799999999999999987754 3 88876

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=6.6e-13  Score=62.41  Aligned_cols=42  Identities=26%  Similarity=0.468  Sum_probs=37.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..+|||+|||..+++++|+++|++||.|.+++++.+.. .++|
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg   49 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKG   49 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcc
Confidence            45799999999999999999999999999999998864 3455

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=2e-13  Score=63.66  Aligned_cols=35  Identities=29%  Similarity=0.618  Sum_probs=33.4

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        19 l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      |||+|||.++++++|+++|++||.|.+++++.++.
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

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.36  E-value=1.8e-12  Score=60.21  Aligned_cols=41  Identities=24%  Similarity=0.446  Sum_probs=36.4

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        12 ~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..+.+++|||+|||..+++++|.++|+.||.|.+++++.++
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~   44 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR   44 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc
Confidence            34457899999999999999999999999999999987654

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1.3e-12  Score=62.78  Aligned_cols=45  Identities=20%  Similarity=0.380  Sum_probs=38.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC--CCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD--GTSKER   59 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~--g~~rG~   59 (59)
                      ...++|||+|||+.+++++|+++|+.|| +.++.++.+..  |+++|.
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~   59 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF   59 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCccee
Confidence            3457999999999999999999999999 77888877764  777773

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=4e-13  Score=69.31  Aligned_cols=44  Identities=32%  Similarity=0.699  Sum_probs=40.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||||||+.+++++|+++|++||.|.++.++.+.. |+++|
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g   49 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG   49 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccC
Confidence            347899999999999999999999999999999999987 87766

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.33  E-value=1.4e-14  Score=68.68  Aligned_cols=46  Identities=15%  Similarity=0.279  Sum_probs=40.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      +....+|||+|||+.+++++|+++|+.||.|.+++++.+..|++||
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg   55 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK   55 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTT
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccE
Confidence            4456789999999999999999999999999998887665588887

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.33  E-value=1e-12  Score=60.14  Aligned_cols=38  Identities=26%  Similarity=0.315  Sum_probs=35.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG   54 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g   54 (59)
                      .+|||+|||+++++++|+++|++||.|.++++..++.+
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            37999999999999999999999999999999998763

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=3.8e-12  Score=60.36  Aligned_cols=40  Identities=20%  Similarity=0.422  Sum_probs=35.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ...+++|||+|||+.+++++|+++|++||.|..+.+..+.
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~   50 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR   50 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccc
Confidence            3467789999999999999999999999999998876553

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=1.3e-12  Score=61.26  Aligned_cols=37  Identities=24%  Similarity=0.520  Sum_probs=33.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..++|||+|||+.+++++|+++|++||.|.++++..+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~   40 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP   40 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec
Confidence            4679999999999999999999999999999987654

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=8.6e-13  Score=62.11  Aligned_cols=42  Identities=24%  Similarity=0.391  Sum_probs=36.7

Q ss_pred             CCCeEEEcCCCCCCcHHHH---HHhhccCCCeEEEEEEeCCC-CCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDV---RKIFAPFGTIEECTVLKGPD-GTS   56 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l---~~~F~~~G~i~~~~v~~d~~-g~~   56 (59)
                      ....|||+|||+.+++++|   .++|++||+|.++.+++|+. +.+
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~   52 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGS   52 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSS
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCC
Confidence            4567999999999999999   67899999999999999976 443

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=4.6e-12  Score=59.19  Aligned_cols=38  Identities=32%  Similarity=0.594  Sum_probs=34.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++|||+|||..+++++|+++|++||.|.++++..++
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k   44 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK   44 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc
Confidence            45689999999999999999999999999999988764

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=3.2e-12  Score=60.86  Aligned_cols=39  Identities=26%  Similarity=0.532  Sum_probs=35.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +..++|||+|||..+++++|+++|++||.|.+++++.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~k   54 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK   54 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc
Confidence            346789999999999999999999999999999998774

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=9.2e-12  Score=59.81  Aligned_cols=45  Identities=13%  Similarity=0.115  Sum_probs=38.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      .....|||+|||+.+++++|+++|+.+|.+....++.+.. ++++|
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG   58 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG   58 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcce
Confidence            3566799999999999999999999999988866665555 88776

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=2.9e-12  Score=61.96  Aligned_cols=39  Identities=23%  Similarity=0.328  Sum_probs=35.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ....+|||+|||+.+++++|+++|++||.|.++.++.++
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~   43 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN   43 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC
Confidence            456689999999999999999999999999999998765

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.9e-13  Score=65.44  Aligned_cols=46  Identities=24%  Similarity=0.286  Sum_probs=40.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ....++|||+|||..+++++|+++|++||.|..+.++.+.. |+++|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g   61 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG   61 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccc
Confidence            34578999999999999999999999999999998888766 77776

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.4e-12  Score=61.02  Aligned_cols=35  Identities=14%  Similarity=0.217  Sum_probs=32.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .+|||+|||+.+++++|+++|++||.|.++++..|
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~   35 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   35 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc
Confidence            36999999999999999999999999999998665

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=5.6e-12  Score=60.06  Aligned_cols=45  Identities=18%  Similarity=0.358  Sum_probs=37.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeE--------EEEEEeCCC-CCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE--------ECTVLKGPD-GTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~--------~~~v~~d~~-g~~rG   58 (59)
                      ....+|||+|||..+++++|+++|+.||.|.        .+.+..|+. |+++|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g   59 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG   59 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccc
Confidence            4577999999999999999999999999874        456667766 77776

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.6e-11  Score=57.34  Aligned_cols=40  Identities=28%  Similarity=0.455  Sum_probs=35.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .+..+.|||+|||..+++++|+++|++||.|.++++..++
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~   44 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK   44 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc
Confidence            3467899999999999999999999999999999887654

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=2.2e-11  Score=62.64  Aligned_cols=44  Identities=27%  Similarity=0.558  Sum_probs=40.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCC-CCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSKE   58 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~-g~~rG   58 (59)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.|.. |+++|
T Consensus        96 ~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g  140 (183)
T d1u1qa_          96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG  140 (183)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             ccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccce
Confidence            567899999999999999999999999999999999987 87776

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=2.4e-11  Score=57.76  Aligned_cols=38  Identities=29%  Similarity=0.533  Sum_probs=34.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++|||+|||..+++++|+++|++||.|..+++..++
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~   53 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD   53 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc
Confidence            46799999999999999999999999999999987654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.1e-11  Score=59.40  Aligned_cols=45  Identities=9%  Similarity=0.020  Sum_probs=37.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC-CCCCCCCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG-PDGTSKER   59 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d-~~g~~rG~   59 (59)
                      ....|||+|||+++++++|+++|+.||.+....++.+ ..|+++|.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~   52 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ   52 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCcc
Confidence            4457999999999999999999999999887544444 44998884

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.2e-11  Score=59.57  Aligned_cols=37  Identities=16%  Similarity=0.357  Sum_probs=33.5

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         16 DKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        16 ~~~l~v~~L~~-~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ++.|||+||++ .+++++|+++|+.||.|.++.++.++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~   39 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK   39 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc
Confidence            56899999965 58999999999999999999999875

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=2e-11  Score=58.48  Aligned_cols=44  Identities=20%  Similarity=0.380  Sum_probs=37.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      .....|||+|||+++++++|+++|+.|| +.++.++.+..|+++|
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G   56 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTG   56 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceE
Confidence            4567899999999999999999999998 5578888887776665

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.17  E-value=5.3e-11  Score=56.73  Aligned_cols=37  Identities=19%  Similarity=0.222  Sum_probs=33.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ...+|||+|||+.+++++|+++|+.||.|.++.+..+
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            4568999999999999999999999999999987643

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.17  E-value=1.4e-11  Score=59.46  Aligned_cols=35  Identities=11%  Similarity=0.301  Sum_probs=31.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ..++|||+|||..+++++|+++|+.||.|.++.+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~   43 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP   43 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee
Confidence            34689999999999999999999999999998774

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=5.4e-12  Score=61.40  Aligned_cols=48  Identities=17%  Similarity=0.377  Sum_probs=38.1

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe-CCCCCCCC
Q psy10283         11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK-GPDGTSKE   58 (59)
Q Consensus        11 ~~~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~-d~~g~~rG   58 (59)
                      .+......|||+|||+.+++++|+++|+.||.+..+.++. +..|+++|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G   61 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG   61 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEE
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceee
Confidence            3444677899999999999999999999999987654444 44487766

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.16  E-value=9.8e-11  Score=56.16  Aligned_cols=39  Identities=21%  Similarity=0.178  Sum_probs=35.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +..+.|||+|||..+++++|.++|++||.|.++.+.+++
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k   51 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK   51 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc
Confidence            357789999999999999999999999999999887653

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.15  E-value=4.9e-12  Score=58.88  Aligned_cols=45  Identities=13%  Similarity=0.170  Sum_probs=36.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEE-EEEeCCCCCCCC
Q psy10283         14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPDGTSKE   58 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~-~v~~d~~g~~rG   58 (59)
                      +....|||+|||+++++++|+++|+.||.+... .+..+..|+++|
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G   52 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG   52 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcce
Confidence            456679999999999999999999999998764 555555577765

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=8.4e-11  Score=54.82  Aligned_cols=38  Identities=16%  Similarity=0.309  Sum_probs=33.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..+.|||+|||..+++++|+++|++||.+.++.+..+.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~   46 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK   46 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec
Confidence            36789999999999999999999999999988766543

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.13  E-value=5e-11  Score=56.88  Aligned_cols=38  Identities=16%  Similarity=0.364  Sum_probs=33.9

Q ss_pred             CCCeEEEcCCCCC-CcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v~~L~~~-~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      .++.|||+|||.. +++++|.++|++||.|.++.++.++
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k   55 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK   55 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC
Confidence            4678999999985 8999999999999999999988664

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=5.5e-11  Score=54.61  Aligned_cols=38  Identities=21%  Similarity=0.245  Sum_probs=33.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        13 ~~~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      +..+++|||+|++  +++++|+++|++||.|.++++..++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~   39 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR   39 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC
Confidence            3467899999986  8999999999999999999987654

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.11  E-value=6.5e-11  Score=55.55  Aligned_cols=39  Identities=13%  Similarity=0.263  Sum_probs=34.5

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~~-~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ..++.|||+|||.. +++++|.++|++||.|.++.++.++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k   45 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI   45 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc
Confidence            45678999999986 7899999999999999999987664

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=3.7e-11  Score=58.50  Aligned_cols=37  Identities=24%  Similarity=0.378  Sum_probs=33.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      -..+||||||..+|+++|+++|++||+|..+.++.++
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k   47 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA   47 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC
Confidence            3456999999999999999999999999999998664

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=2.4e-11  Score=56.00  Aligned_cols=35  Identities=31%  Similarity=0.413  Sum_probs=31.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .+|||+|||.++++++|+++|++||.+.++++...
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~   36 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK   36 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc
Confidence            47999999999999999999999999887766654

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=2.2e-10  Score=54.54  Aligned_cols=36  Identities=31%  Similarity=0.637  Sum_probs=31.2

Q ss_pred             CCCCeEEEcCCC-CCCcHHHHHHhhccCCCeEEEEEE
Q psy10283         14 PPDKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTVL   49 (59)
Q Consensus        14 ~~~~~l~v~~L~-~~~~~~~l~~~F~~~G~i~~~~v~   49 (59)
                      ....+|||+||+ ..+++++|+++|++||.|.++++.
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            346789999997 578889999999999999999874

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=3.9e-10  Score=52.28  Aligned_cols=37  Identities=24%  Similarity=0.119  Sum_probs=32.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      ..++|||+|||..+++++|+++|++||.+..+.+...
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~   43 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI   43 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc
Confidence            4578999999999999999999999999888776543

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=6.4e-12  Score=58.96  Aligned_cols=32  Identities=19%  Similarity=0.299  Sum_probs=28.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      ++|||||||..+++++|+++|++||.+..+.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~   33 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ   33 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEE
Confidence            68999999999999999999999998776654

>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=98.92  E-value=3.8e-10  Score=53.34  Aligned_cols=33  Identities=21%  Similarity=0.307  Sum_probs=29.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEEEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECT   47 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~   47 (59)
                      ..++|||+|||+.+++++|+++|++||.|..++
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~   47 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVS   47 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeee
Confidence            467899999999999999999999999887654

>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=98.90  E-value=1.1e-09  Score=51.24  Aligned_cols=35  Identities=26%  Similarity=0.621  Sum_probs=30.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHH----hhccCCCeEEEEEEe
Q psy10283         16 DKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLK   50 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~----~F~~~G~i~~~~v~~   50 (59)
                      .++|||+|||..+++++|++    +|++||+|.++++..
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            57899999999999988864    689999999987643

>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=98.87  E-value=7.6e-10  Score=52.90  Aligned_cols=38  Identities=13%  Similarity=0.257  Sum_probs=32.9

Q ss_pred             CCCeEEE--cCCCCCCcHHHHHHhhccCCCeEEEEEEeCC
Q psy10283         15 PDKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        15 ~~~~l~v--~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ....+||  |+||..+++++|+++|++||.|.++.++.++
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k   56 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK   56 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc
Confidence            4567888  5599999999999999999999999877654

>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=98.84  E-value=4.2e-09  Score=47.76  Aligned_cols=29  Identities=14%  Similarity=0.450  Sum_probs=25.5

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeEEEEE
Q psy10283         19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTV   48 (59)
Q Consensus        19 l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v   48 (59)
                      |||+|||+++++++|+++|++|| +..+.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~   29 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV   29 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee
Confidence            79999999999999999999999 555444

>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=98.83  E-value=4.2e-09  Score=49.02  Aligned_cols=27  Identities=15%  Similarity=0.342  Sum_probs=25.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCC
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFG   41 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G   41 (59)
                      ...+|||+|||..+++++|+++|++||
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G   30 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD   30 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC
Confidence            456899999999999999999999999

>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=98.54  E-value=1.9e-08  Score=48.12  Aligned_cols=39  Identities=10%  Similarity=0.159  Sum_probs=31.8

Q ss_pred             CCCCeEEEcCCCCCC-cH----HHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGMLSKQQ-NE----DDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L~~~~-~~----~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ....+|||+||+..+ ++    ++|+++|++||.|.++++++..
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~   46 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF   46 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC
Confidence            356789999999886 33    5689999999999999987653

>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=98.51  E-value=6.7e-10  Score=53.37  Aligned_cols=42  Identities=12%  Similarity=0.079  Sum_probs=36.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeCCCCCCCC
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE   58 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d~~g~~rG   58 (59)
                      ..+++.+++..++++.|+++|++||+|.+++|+.+..|++||
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G   69 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG   69 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEee
Confidence            357788888889999999999999999999998876688876

>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=98.41  E-value=1.2e-07  Score=43.53  Aligned_cols=35  Identities=17%  Similarity=0.118  Sum_probs=29.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        16 ~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      .+.|+|+++|+..+++.|+ .|++||.|.++++..+
T Consensus         4 ~~wV~V~G~p~~~~~~il~-~F~~~G~I~~~~~~~~   38 (81)
T d1wwha1           4 DTWVTVFGFPQASASYILL-QFAQYGNILKHVMSNT   38 (81)
T ss_dssp             GGEEEEECCCGGGHHHHHH-HHHTTSCEEEEEECSS
T ss_pred             ccEEEEECCChHHHHHHHH-HHHhhhhhheEEecCC
Confidence            5689999999999877665 7999999999987544

>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=97.27  E-value=0.00012  Score=34.36  Aligned_cols=39  Identities=18%  Similarity=0.324  Sum_probs=29.4

Q ss_pred             CCCeEEEcCC--CCCC--------cHHHHHHhhccCCCeEEEEEEeCCC
Q psy10283         15 PDKKLFVGML--SKQQ--------NEDDVRKIFAPFGTIEECTVLKGPD   53 (59)
Q Consensus        15 ~~~~l~v~~L--~~~~--------~~~~l~~~F~~~G~i~~~~v~~d~~   53 (59)
                      ..+-|.+.|+  +...        ..+++++.|++||.|.++.|+++.+
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~   51 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVD   51 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTT
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCC
Confidence            3566888998  3333        2246888999999999999988765

>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=97.09  E-value=0.00053  Score=31.80  Aligned_cols=39  Identities=13%  Similarity=0.288  Sum_probs=29.5

Q ss_pred             CCCCeEEEcCC--CCCCc---------HHHHHHhhccCCCeEEEEEEeCC
Q psy10283         14 PPDKKLFVGML--SKQQN---------EDDVRKIFAPFGTIEECTVLKGP   52 (59)
Q Consensus        14 ~~~~~l~v~~L--~~~~~---------~~~l~~~F~~~G~i~~~~v~~d~   52 (59)
                      ...+.|++.|+  |.+..         .+++++.|++||.|..+.+..+.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~   55 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH   55 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC
Confidence            35678999998  43321         25788899999999999887664

>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=94.66  E-value=0.062  Score=24.52  Aligned_cols=34  Identities=9%  Similarity=0.235  Sum_probs=28.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEe
Q psy10283         17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   50 (59)
Q Consensus        17 ~~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~   50 (59)
                      .+|-|.+||+..+++++.+.++..|++.-.....
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~   35 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFS   35 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeC
Confidence            4788999999999999999999998877655443

>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=94.49  E-value=0.036  Score=25.81  Aligned_cols=31  Identities=19%  Similarity=0.414  Sum_probs=26.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHhhccCCCeEE
Q psy10283         15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE   45 (59)
Q Consensus        15 ~~~~l~v~~L~~~~~~~~l~~~F~~~G~i~~   45 (59)
                      ....+|.-.-|......+|.++|++||.|.-
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V   44 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI   44 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCC
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEE
Confidence            4567888889999999999999999998753

>d1qyra_ c.66.1.24 (A:) High level kasugamycin resistance protein KsgA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: rRNA adenine dimethylase-like
domain: High level kasugamycin resistance protein KsgA
species: Escherichia coli [TaxId: 562]

Probab=85.86  E-value=0.74  Score=24.17  Aligned_cols=34  Identities=12%  Similarity=0.082  Sum_probs=26.7

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCCeEEEEEEeC
Q psy10283         18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   51 (59)
Q Consensus        18 ~l~v~~L~~~~~~~~l~~~F~~~G~i~~~~v~~d   51 (59)
                      -..|||||+.++..-+..+......+..+.+|..
T Consensus        92 ~~vvgNlPY~Iss~Il~~l~~~~~~~~~~~~m~Q  125 (252)
T d1qyra_          92 LRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQ  125 (252)
T ss_dssp             EEEEEECCTTTHHHHHHHHHTTGGGEEEEEEEEE
T ss_pred             eEEEecchHHHHHHHHHHhcccccceehhhhhhh
Confidence            4667999999999988888776666777766654