Citrus Sinensis ID: 030010

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180----
Protein Sequence
MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASEAMQTN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHcccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccHHHHHcccccccccccccccccEEEEEcccccccHHHHHHHHHHHcHHHHEEEEEcccccccccEEEEEEcHHHHHHHHHHHcccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MFADQVSAFPVQQAGRASAIETGTKLYISnldygvsnEDIKELFSEvgdlkrysihydrsgrskgtAEVVYSRRADAVAAVKRYnnvqldgkpmkieivgtniatrtaapaanvnfgnsngvprggqgrggafrrlrgggggggrgfgrgrgrgrernekisaEDLDADLDKYYSEASEAMQTN
Flexible Loop (DISEMBL)
mfadqvsafpvqqagrasaietGTKLYISNLDYGVSNEDIKELFSevgdlkrysihydrsgrskgtaevVYSRRADAVAAVKrynnvqldgkpmKIEIVGTNIATRtaapaanvnfgnsngvprggqGRGGAFrrlrgggggggrgfgrgrgrgrernekisaedldadlDKYYSEASEAMQTN
Low Complexity Region (SEG)
MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPrggqgrggafrrlrgggggggrgfgrgrgrgrerNEKISAEDLDADLDKYYSEASEAMQTN
Disordered region (IsUnstruct)
******************AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRT*****************************************************************************
Disordered Region (DISOPRED)
**************************YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE*********************************************************************DADLDKYYSE********
Disordered Region (DISEMBL)
MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD***********VYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSE********
Disordered Region (DISPRO)
********************ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAA***************************************************EDLDADLDKYYSEASE*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASEAMQTN
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	184	2.2.26 [Sep-21-2011]
Q28FB9	260	THO complex subunit 4 OS=	yes	no	0.788	0.557	0.464	2e-27
Q58EA2	256	THO complex subunit 4-A O	N/A	no	0.788	0.566	0.467	2e-27
B5FXN8	254	THO complex subunit 4 OS=	yes	no	0.815	0.590	0.484	2e-26
Q3T0I4	257	THO complex subunit 4 OS=	yes	no	0.760	0.544	0.490	1e-24
Q6GLW1	256	THO complex subunit 4-B O	N/A	no	0.788	0.566	0.422	2e-24
O08583	255	THO complex subunit 4 OS=	no	no	0.5	0.360	0.559	3e-24
Q86V81	257	THO complex subunit 4 OS=	yes	no	0.760	0.544	0.483	4e-24
Q9JJW6	218	RNA and export factor-bin	no	no	0.456	0.385	0.583	6e-24
Q9BY77	421	Polymerase delta-interact	no	no	0.380	0.166	0.447	3e-11
Q8BG81	420	Polymerase delta-interact	no	no	0.402	0.176	0.444	3e-11

>sp|Q28FB9|THOC4_XENTR THO complex subunit 4 OS=Xenopus tropicalis GN=alyref PE=2 SV=1

 Score =  122 bits (305), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 78/168 (46%), Positives = 103/168 (61%), Gaps = 23/168 (13%)

Query: 15  GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
           G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct: 100 GTGAGMETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 159

Query: 75  ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFR 134
           ADA+ A+K+YN V LDG+PM I++V + I  +                P   Q RGG   
Sbjct: 160 ADALKAMKQYNGVPLDGRPMNIQLVTSQIEAQRR--------------PIQSQSRGGGIT 205

Query: 135 RLRGGGGG---------GGRGFGRGRGRGRERNEKISAEDLDADLDKY 173
           R RGG  G          G   GRGRG GR   +++SAE+LDA LD Y
Sbjct: 206 RPRGGAIGFSGANRRGGRGGNRGRGRGAGRNPKQQLSAEELDAQLDAY 253

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.
Xenopus tropicalis (taxid: 8364)

>sp|Q58EA2|THO4A_XENLA THO complex subunit 4-A OS=Xenopus laevis GN=alyref-a PE=2 SV=1

 Score =  121 bits (304), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 78/167 (46%), Positives = 103/167 (61%), Gaps = 22/167 (13%)

Query: 15  GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
           G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct: 97  GAGAGMETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 156

Query: 75  ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFR 134
           ADA+ A+K+YN V LDG+PM I++V + I  +                P   Q RGG   
Sbjct: 157 ADALKAMKQYNGVPLDGRPMNIQLVTSQIEAQRR--------------PIQSQSRGGGVT 202

Query: 135 RLRGGGGG--------GGRGFGRGRGRGRERNEKISAEDLDADLDKY 173
           R RGG  G         G   GRGRG GR   +++SAE+LDA LD Y
Sbjct: 203 RPRGGTLGFASGNRRGRGGNRGRGRGAGRNPKQQLSAEELDAQLDAY 249

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus laevis (taxid: 8355)

>sp|B5FXN8|THOC4_TAEGU THO complex subunit 4 OS=Taeniopygia guttata GN=ALYREF PE=2 SV=1

 Score =  118 bits (296), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/163 (48%), Positives = 105/163 (64%), Gaps = 13/163 (7%)

Query: 15  GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
           G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct: 94  GAGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 153

Query: 75  ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFR 134
           ADA+ A+K+YN V LDG+PM I++V + I T+   PA +VN        RGG  R     
Sbjct: 154 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQR-RPAQSVN--------RGGMTRNRGVL 204

Query: 135 RLRGGGGGGGRGFGRGRGRGRER----NEKISAEDLDADLDKY 173
              GGGG      G  RGRGR       +++SAE+LDA LD Y
Sbjct: 205 GGFGGGGNRRGTRGGNRGRGRGAGRTSKQQLSAEELDAQLDAY 247

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Taeniopygia guttata (taxid: 59729)

>sp|Q3T0I4|THOC4_BOVIN THO complex subunit 4 OS=Bos taurus GN=ALYREF PE=2 SV=1

 Score =  112 bits (281), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 75/153 (49%), Positives = 99/153 (64%), Gaps = 13/153 (8%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+ADA+ A+K+Y
Sbjct: 107 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 166

Query: 85  NNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRG----GAFRRLRGGG 140
           N V LDG+PM I++V + I T+   PA +VN        RGG  R     G         
Sbjct: 167 NGVPLDGRPMNIQLVTSQIDTQR-RPAQSVN--------RGGMTRNRGSGGFGGGGGTRR 217

Query: 141 GGGGRGFGRGRGRGRERNEKISAEDLDADLDKY 173
           G  G   GRGRG GR   +++SAE+LDA LD Y
Sbjct: 218 GTRGGSRGRGRGTGRSSKQQLSAEELDAQLDAY 250

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Bos taurus (taxid: 9913)

>sp|Q6GLW1|THO4B_XENLA THO complex subunit 4-B OS=Xenopus laevis GN=alyref-b PE=2 SV=1

 Score =  111 bits (278), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 23/168 (13%)

Query: 15  GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
           G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct: 96  GTGAGMETGGKLLVSNLDFGVSDADIQELFAEFGSLKKAAVHYDRSGRSLGTADVHFERK 155

Query: 75  ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFR 134
           ADA+ A+K+YN V LDG+ M I++V + I  +                P   Q RGG   
Sbjct: 156 ADALKAMKQYNGVPLDGRSMNIQLVTSQIEAQRR--------------PIQSQSRGGGVA 201

Query: 135 RLRGGGGGGGRGFGRGRGRGRER---------NEKISAEDLDADLDKY 173
           R RGG  G   G  R                  +++SAE+LDA LD Y
Sbjct: 202 RPRGGAIGFAAGGNRRDRGANRGRGRGAGRNPKQQLSAEELDAQLDAY 249

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus laevis (taxid: 8355)

>sp|O08583|THOC4_MOUSE THO complex subunit 4 OS=Mus musculus GN=Alyref PE=1 SV=3

 Score =  111 bits (277), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/93 (55%), Positives = 73/93 (78%), Gaps = 1/93 (1%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+ADA+ A+K+Y
Sbjct: 106 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 165

Query: 85  NNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
           N V LDG+PM I++V + I T+   PA ++N G
Sbjct: 166 NGVPLDGRPMNIQLVTSQIDTQR-RPAQSINRG 197

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Plays a role in mRNA processing and export. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Mus musculus (taxid: 10090)

>sp|Q86V81|THOC4_HUMAN THO complex subunit 4 OS=Homo sapiens GN=ALYREF PE=1 SV=3

 Score =  110 bits (276), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 74/153 (48%), Positives = 98/153 (64%), Gaps = 13/153 (8%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+ADA+ A+K+Y
Sbjct: 107 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 166

Query: 85  NNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFRRLRGGGGGGG 144
           N V LDG+PM I++V + I  +   PA +VN        RGG  R        GGGG   
Sbjct: 167 NGVPLDGRPMNIQLVTSQIDAQR-RPAQSVN--------RGGMTRNRGAGGFGGGGGTRR 217

Query: 145 RGFGRGRGRGRER----NEKISAEDLDADLDKY 173
              G  RGRGR       +++SAE+LDA LD Y
Sbjct: 218 GTRGGARGRGRGAGRNSKQQLSAEELDAQLDAY 250

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay. Directs mRNA derived from Herpes simplex virus intron-less genes to the NXF1-mediated export pathway.

Homo sapiens (taxid: 9606)

>sp|Q9JJW6|REFP2_MOUSE RNA and export factor-binding protein 2 OS=Mus musculus GN=Refbp2 PE=1 SV=1

 Score =  110 bits (275), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 49/84 (58%), Positives = 67/84 (79%)

Query: 20  IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVA 79
           +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++ YDRSGRS GTA+V + RRADA+ 
Sbjct: 71  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 130

Query: 80  AVKRYNNVQLDGKPMKIEIVGTNI 103
           A+K+Y  V LDG+PM I++V + I
Sbjct: 131 AMKQYKGVPLDGRPMDIQLVASQI 154

Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation (By similarity). Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Mus musculus (taxid: 10090)

>sp|Q9BY77|PDIP3_HUMAN Polymerase delta-interacting protein 3 OS=Homo sapiens GN=POLDIP3 PE=1 SV=2

 Score = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 47/76 (61%), Gaps = 6/76 (7%)

Query: 23  GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
           GTK+ ++NL   V+ EDI ELF   G LKR  + +       G AEVV+ ++ DA+ A K
Sbjct: 279 GTKMTVNNLHPRVTEEDIVELFCVCGALKRARLVH------PGVAEVVFVKKDDAITAYK 332

Query: 83  RYNNVQLDGKPMKIEI 98
           +YNN  LDG+PMK  +
Sbjct: 333 KYNNRCLDGQPMKCNL 348

Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized mRNA.

Homo sapiens (taxid: 9606)

>sp|Q8BG81|PDIP3_MOUSE Polymerase delta-interacting protein 3 OS=Mus musculus GN=Poldip3 PE=2 SV=1

 Score = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/81 (44%), Positives = 50/81 (61%), Gaps = 7/81 (8%)

Query: 18  SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADA 77
           S +E GTK+ ++NL   V+ EDI ELF   G LKR  + +       G AEVV+ ++ DA
Sbjct: 275 SPLE-GTKMTVNNLHPRVTEEDIVELFCVCGALKRARLVH------PGVAEVVFVKKDDA 327

Query: 78  VAAVKRYNNVQLDGKPMKIEI 98
           + A K+YNN  LDG+PMK  +
Sbjct: 328 ITAYKKYNNRCLDGQPMKCNL 348

Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized 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	184
225435024	243	PREDICTED: RNA and export factor-binding	0.967	0.732	0.794	3e-60
255581121	247	RNA and export factor binding protein, p	0.896	0.668	0.828	2e-59
356550261	243	PREDICTED: THO complex subunit 4-A-like	0.967	0.732	0.688	2e-59
449450684	237	PREDICTED: RNA and export factor-binding	0.945	0.734	0.724	3e-57
356542471	247	PREDICTED: RNA and export factor-binding	0.978	0.728	0.675	5e-57
147843918	281	hypothetical protein VITISV_023787 [Viti	0.967	0.633	0.609	7e-57
356539036	247	PREDICTED: RNA and export factor-binding	0.978	0.728	0.670	4e-56
357472739	376	THO complex subunit [Medicago truncatula	0.918	0.449	0.706	7e-54
51490665	252	ALY protein [Nicotiana benthamiana]	0.978	0.714	0.689	1e-52
449462627	237	PREDICTED: RNA and export factor-binding	0.940	0.729	0.663	5e-52

>gi|225435024|ref|XP_002284215.1| PREDICTED: RNA and export factor-binding protein 2 [Vitis vinifera] gi|297746115|emb|CBI16171.3| unnamed protein product [Vitis vinifera]

 Score =  236 bits (602), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 147/185 (79%), Positives = 155/185 (83%), Gaps = 7/185 (3%)

Query: 1   MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS 60
           MFADQ +A+P Q AGR SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS
Sbjct: 65  MFADQAAAYPAQ-AGRTSAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS 123

Query: 61  GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAA-PAANVNFGNS 119
           GRSKGTAEVV+SRR DAVAAVKRYNNVQLDGKPMKIEIVGTNIAT  A  P  N  FGNS
Sbjct: 124 GRSKGTAEVVFSRRGDAVAAVKRYNNVQLDGKPMKIEIVGTNIATPAAVPPVTNGTFGNS 183

Query: 120 NGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASE 179
           NG  R  QGR G+  + R  GG GGRGFGRGRGRGR R EK+SAEDLDADL+KY+   SE
Sbjct: 184 NGGLRSAQGRVGS--QGRPRGGSGGRGFGRGRGRGRGRGEKVSAEDLDADLEKYH---SE 238

Query: 180 AMQTN 184
           AMQ N
Sbjct: 239 AMQIN 243

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581121|ref|XP_002531375.1| RNA and export factor binding protein, putative [Ricinus communis] gi|223529035|gb|EEF31023.1| RNA and export factor binding protein, putative [Ricinus communis]

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 140/169 (82%), Positives = 146/169 (86%), Gaps = 4/169 (2%)

Query: 16  RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRA 75
           RAS IETGTKLYISNL+YGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVV+SRR 
Sbjct: 83  RASGIETGTKLYISNLEYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVFSRRT 142

Query: 76  DAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGAFRR 135
           DA+AAVKRYNNVQLDGKPMKIEIVGTNIAT  A PAAN NFGNSNG PRGGQGRGG  RR
Sbjct: 143 DALAAVKRYNNVQLDGKPMKIEIVGTNIATPAATPAANGNFGNSNGAPRGGQGRGGTMRR 202

Query: 136 LRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASEAMQTN 184
            RG    G    GRGRGRGR R EK+SAEDLDADL+KY+   SEAMQTN
Sbjct: 203 PRGASSDGRGF-GRGRGRGRGRGEKVSAEDLDADLEKYH---SEAMQTN 247

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550261|ref|XP_003543506.1| PREDICTED: THO complex subunit 4-A-like [Glycine max]

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 128/186 (68%), Positives = 146/186 (78%), Gaps = 8/186 (4%)

Query: 1   MFADQ--VSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD 58
           M+A+Q   +A+P    GRAS+IETGTKLYISNLDYGVSN+DIKELF EVGD+KR+++HYD
Sbjct: 64  MYANQPVAAAYP---GGRASSIETGTKLYISNLDYGVSNDDIKELFLEVGDVKRHTVHYD 120

Query: 59  RSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGN 118
           RSGRSKGTAEVV+SRRADAVAAVKRYNNVQLDGKPMK+EIVGTNIAT  A PA N  FGN
Sbjct: 121 RSGRSKGTAEVVFSRRADAVAAVKRYNNVQLDGKPMKVEIVGTNIATHAAPPAVNGTFGN 180

Query: 119 SNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEAS 178
             GVPR GQGR G+  R RGG  G G            R+EK+SAEDLDADL+KY+   +
Sbjct: 181 PTGVPRSGQGRSGSLGRPRGGSRGRGSIQRGRGRGRGGRDEKVSAEDLDADLEKYH---A 237

Query: 179 EAMQTN 184
           EAMQ N
Sbjct: 238 EAMQLN 243

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450684|ref|XP_004143092.1| PREDICTED: RNA and export factor-binding protein 2-like [Cucumis sativus] gi|449508143|ref|XP_004163231.1| PREDICTED: RNA and export factor-binding protein 2-like [Cucumis sativus]

 Score =  226 bits (576), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 134/185 (72%), Positives = 147/185 (79%), Gaps = 11/185 (5%)

Query: 1   MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS 60
           MFAD  S F VQ  GRASAI+TGTKLYISNLDYGVSNEDIKELFSEVGD+KR+ IHYD+S
Sbjct: 63  MFADPSSGFLVQ-GGRASAIQTGTKLYISNLDYGVSNEDIKELFSEVGDMKRHGIHYDKS 121

Query: 61  GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVN-FGNS 119
           GRSKGTAEVV+SRR DAVAAVK+YNNVQLDGKPMKIEIVGTNI+T    P A VN F NS
Sbjct: 122 GRSKGTAEVVFSRRLDAVAAVKKYNNVQLDGKPMKIEIVGTNISTPAVGPTAAVNPFENS 181

Query: 120 NGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASE 179
           NG PR  QGRGG            G GFGRGRGRGR  +EK+SAEDLDADL+KY+   +E
Sbjct: 182 NGAPRRQQGRGGP------PSRQRGHGFGRGRGRGRGPSEKVSAEDLDADLEKYH---AE 232

Query: 180 AMQTN 184
           +MQ N
Sbjct: 233 SMQIN 237

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542471|ref|XP_003539690.1| PREDICTED: RNA and export factor-binding protein 2-like [Glycine max]

 Score =  225 bits (574), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 127/188 (67%), Positives = 145/188 (77%), Gaps = 8/188 (4%)

Query: 1   MFADQVSA---FPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHY 57
           ++ADQ  A   +P Q  GRA++IETGTKLYISNLDYGVSN+DIKELF+EVGDLKR+++HY
Sbjct: 64  LYADQHVAAAGYPAQ-GGRAASIETGTKLYISNLDYGVSNDDIKELFAEVGDLKRHAVHY 122

Query: 58  DRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
           DRSGRSKGTAEVV+SRRADAV+AVKRYNNVQLDGKPMKIEIVGTNI+T   APA N   G
Sbjct: 123 DRSGRSKGTAEVVFSRRADAVSAVKRYNNVQLDGKPMKIEIVGTNISTPGVAPAPNGAIG 182

Query: 118 NSNGVPRGGQGRGGAF-RRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSE 176
           N NGVPR GQGRGGA  R    G G            G  R EK+SA+DLDADL+KY+  
Sbjct: 183 NFNGVPRSGQGRGGALRRPGGRGQGIRRDRGRGRGRGGGGRGEKVSADDLDADLEKYH-- 240

Query: 177 ASEAMQTN 184
            +EAMQ N
Sbjct: 241 -AEAMQLN 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147843918|emb|CAN83715.1| hypothetical protein VITISV_023787 [Vitis vinifera]

 Score =  225 bits (573), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 136/223 (60%), Positives = 146/223 (65%), Gaps = 45/223 (20%)

Query: 1   MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS 60
           MFADQ +A+P Q AGR SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS
Sbjct: 65  MFADQAAAYPAQ-AGRTSAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS 123

Query: 61  GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAA-PAANVNFGNS 119
           GRSKGTAEVV+SRR DAVAAVKRYNNVQLDGKPMKIEIVGTNIAT  A  P  N  FGNS
Sbjct: 124 GRSKGTAEVVFSRRGDAVAAVKRYNNVQLDGKPMKIEIVGTNIATPAAVPPVTNGTFGNS 183

Query: 120 NGVPRGGQGRGGAFRRLRGG----------------GGGGGRGFGRGRGRG--------- 154
           NG  R  + RG    R++                  G     G    +GRG         
Sbjct: 184 NGGLR--RLRGELVHRVKSXPTYFHPSWNALLLVKFGVSWITGLACAQGRGGSQGRPRGG 241

Query: 155 -------------RERNEKISAEDLDADLDKYYSEASEAMQTN 184
                        R R EK+SAEDLDADL+KY+   SEAMQ N
Sbjct: 242 SGGRGFGRGRGRGRGRGEKVSAEDLDADLEKYH---SEAMQIN 281

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539036|ref|XP_003538006.1| PREDICTED: RNA and export factor-binding protein 2-like [Glycine max]

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 126/188 (67%), Positives = 145/188 (77%), Gaps = 8/188 (4%)

Query: 1   MFADQVSA---FPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHY 57
           ++ADQ  A   +P Q  GRA++IETGTKLYISNLDYGVS++DIKELF+EVGDLKR+++HY
Sbjct: 64  LYADQQVAAAGYPAQ-GGRAASIETGTKLYISNLDYGVSSDDIKELFAEVGDLKRHAVHY 122

Query: 58  DRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
           DRSGRSKGTAEVV+SRRADAVAAVKRYNNVQLDGKPMKIEIVGTNI+T   APA N   G
Sbjct: 123 DRSGRSKGTAEVVFSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNISTPGVAPARNGAIG 182

Query: 118 NSNGVPRGGQGRGGAF-RRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSE 176
           N +GVPR GQGRGGA  R    G G            G  R EK+SA+DLDADL+KY+  
Sbjct: 183 NFDGVPRSGQGRGGALRRPGGRGQGVRRDRGRGRGRGGAGRGEKVSADDLDADLEKYH-- 240

Query: 177 ASEAMQTN 184
            +EAMQ N
Sbjct: 241 -AEAMQLN 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472739|ref|XP_003606654.1| THO complex subunit [Medicago truncatula] gi|355507709|gb|AES88851.1| THO complex subunit [Medicago truncatula]

 Score =  215 bits (547), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 130/184 (70%), Positives = 145/184 (78%), Gaps = 15/184 (8%)

Query: 13  QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYS 72
           Q GRA +IETGTKLYISNLDYGVSN+DIKELFSEVGDLKR+ +HYDRSGRSKGTAEVV+S
Sbjct: 196 QGGRAPSIETGTKLYISNLDYGVSNDDIKELFSEVGDLKRHGVHYDRSGRSKGTAEVVFS 255

Query: 73  RRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGGA 132
           RR DAVAAVKRYNNVQLDGKPMKIEIVGTNI+T  AAP  N   GN NG+P+ GQGR G 
Sbjct: 256 RRQDAVAAVKRYNNVQLDGKPMKIEIVGTNISTPGAAPVVNAPIGNFNGIPQSGQGRVGE 315

Query: 133 F------------RRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASEA 180
           F             R RG G GG RG GRG GRGR R++K+SAEDLDA+L+KY+   +EA
Sbjct: 316 FRGPGGRGQGIRRNRGRGRGSGGPRGGGRGGGRGRGRDDKVSAEDLDAELEKYH---AEA 372

Query: 181 MQTN 184
           MQ N
Sbjct: 373 MQLN 376

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51490665|emb|CAG26903.1| ALY protein [Nicotiana benthamiana]

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 131/190 (68%), Positives = 141/190 (74%), Gaps = 10/190 (5%)

Query: 1   MFADQVSAFPVQQAG---RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHY 57
           MFA    AFP  QAG    AS+I TGTKLYISNLDYGVSNEDIKELFSE GDLKRY+IHY
Sbjct: 67  MFAAADQAFPFGQAGGDQAASSISTGTKLYISNLDYGVSNEDIKELFSEAGDLKRYAIHY 126

Query: 58  DRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAAN--VN 115
           DRSGRSKGTAEVV+SRR DA+AAVKRYNNVQLDGKPMKIEIVGTNIAT  AAPA N    
Sbjct: 127 DRSGRSKGTAEVVFSRRQDALAAVKRYNNVQLDGKPMKIEIVGTNIAT-PAAPAFNGAFG 185

Query: 116 FGNSNGVPRGGQG-RGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYY 174
           FG++NG PR  Q   GG  R   G G G G   G       +R EK+SAEDLDADL KY+
Sbjct: 186 FGDTNGGPRTDQARSGGFGRSRGGRGRGRGFRGGSRGRGRGDRGEKVSAEDLDADLMKYH 245

Query: 175 SEASEAMQTN 184
              +EAMQTN
Sbjct: 246 ---TEAMQTN 252

Source: Nicotiana benthamiana

Species: Nicotiana benthamiana

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462627|ref|XP_004149042.1| PREDICTED: RNA and export factor-binding protein 2-like [Cucumis sativus]

 Score =  209 bits (531), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 122/184 (66%), Positives = 139/184 (75%), Gaps = 11/184 (5%)

Query: 1   MFADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS 60
           MF D  +A+P     RASAIETGTKLY+SNLDYGVSNEDIKELFSEVGD+KRYSI+YD+S
Sbjct: 65  MFVDHGAAYP-SHPPRASAIETGTKLYVSNLDYGVSNEDIKELFSEVGDVKRYSINYDKS 123

Query: 61  GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSN 120
           GRSKGTAE+V+SR+ADA+AA+KRYNNVQLDGKPMK+EIVGTNI T      +N +FGN N
Sbjct: 124 GRSKGTAEIVFSRQADALAAIKRYNNVQLDGKPMKLEIVGTNIVTPAVPAPSNASFGNPN 183

Query: 121 GVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKYYSEASEA 180
           G PRGG+  G          GGG    G G G GR   EK+SAEDLDADLDKY+    EA
Sbjct: 184 GFPRGGRAMGRN-------RGGGRGRSGSGSGSGRGHGEKLSAEDLDADLDKYH---EEA 233

Query: 181 MQTN 184
           MQ N
Sbjct: 234 MQIN 237

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	184
TAIR|locus:2181763	292	AT5G02530 [Arabidopsis thalian	0.576	0.363	0.774	4.1e-45
TAIR|locus:2205293	295	AT1G66260 [Arabidopsis thalian	0.554	0.345	0.596	2.7e-34
TAIR|locus:2151779	288	ALY4 "ALWAYS EARLY 4" [Arabido	0.592	0.378	0.554	1.9e-33
UNIPROTKB|Q3T0I4	257	ALYREF "THO complex subunit 4"	0.554	0.396	0.553	1.4e-29
UNIPROTKB|F1PL92	257	ALYREF "Uncharacterized protei	0.554	0.396	0.553	1.4e-29
MGI|MGI:1341044	255	Alyref "Aly/REF export factor"	0.554	0.4	0.543	1.8e-29
UNIPROTKB|E1C2L5	258	THOC4 "Uncharacterized protein	0.581	0.414	0.518	2.3e-29
UNIPROTKB|E9PB61	264	ALYREF "THO complex subunit 4"	0.554	0.386	0.543	4.7e-29
UNIPROTKB|Q86V81	257	ALYREF "THO complex subunit 4"	0.554	0.396	0.543	4.7e-29
ZFIN|ZDB-GENE-070928-29	280	alyref "Aly/REF export factor"	0.559	0.367	0.524	4.7e-29

TAIR|locus:2181763 AT5G02530 [Arabidopsis thaliana (taxid:3702)]

 Score = 410 (149.4 bits), Expect = 4.1e-45, Sum P(2) = 4.1e-45
 Identities = 86/111 (77%), Positives = 94/111 (84%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  S+IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRY IHYDRSGRSKGTAEVV+SRR
Sbjct:    99 GGGSSIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYGIHYDRSGRSKGTAEVVFSRR 158

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAP---AANVNFGNSNGV 122
              DA+AAVKRYNNVQLDGK MKIEIVGTN++   A P    A + F  +NG+
Sbjct:   159 GDALAAVKRYNNVQLDGKLMKIEIVGTNLSA-PALPILATAQIPFP-TNGI 207

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2205293 AT1G66260 [Arabidopsis thaliana (taxid:3702)]

 Score = 334 (122.6 bits), Expect = 2.7e-34, Sum P(2) = 2.7e-34
 Identities = 62/104 (59%), Positives = 84/104 (80%)

Query:    18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADA 77
             S +E GT +YI+NLD GV+NEDI+EL++E+G+LKRY+IHYD++GR  G+AEVVY RR+DA
Sbjct:   101 SGVEVGTTVYITNLDQGVTNEDIRELYAEIGELKRYAIHYDKNGRPSGSAEVVYMRRSDA 160

Query:    78 VAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNG 121
             + A+++YNNV LDG+PMK+EI+G N  T +A  AA VN    NG
Sbjct:   161 IQAMRKYNNVLLDGRPMKLEILGGN--TESAPVAARVNVTGLNG 202

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2151779 ALY4 "ALWAYS EARLY 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 329 (120.9 bits), Expect = 1.9e-33, Sum P(2) = 1.9e-33
 Identities = 61/110 (55%), Positives = 85/110 (77%)

Query:    13 QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYS 72
             +A  AS +E GT+L+++NLD GV+NEDI+ELFSE+G+++RY+IHYD++GR  GTAEVVY 
Sbjct:    82 RAAGASGVEVGTRLHVTNLDQGVTNEDIRELFSEIGEVERYAIHYDKNGRPSGTAEVVYP 141

Query:    73 RRADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPA-ANVNFGNSNG 121
             RR+DA  A+K+YNNV LDG+PM++EI+G N ++        NVN    NG
Sbjct:   142 RRSDAFQALKKYNNVLLDGRPMRLEILGGNNSSEAPLSGRVNVNVTGLNG 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0008150 "biological_process" evidence=ND

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q3T0I4 ALYREF "THO complex subunit 4" [Bos taurus (taxid:9913)]

 Score = 293 (108.2 bits), Expect = 1.4e-29, Sum P(2) = 1.4e-29
 Identities = 57/103 (55%), Positives = 79/103 (76%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:    97 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 156

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
             ADA+ A+K+YN V LDG+PM I++V + I T+   PA +VN G
Sbjct:   157 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQRR-PAQSVNRG 198

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PL92 ALYREF "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 293 (108.2 bits), Expect = 1.4e-29, Sum P(2) = 1.4e-29
 Identities = 57/103 (55%), Positives = 79/103 (76%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:    97 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 156

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
             ADA+ A+K+YN V LDG+PM I++V + I T+   PA +VN G
Sbjct:   157 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQRR-PAQSVNRG 198

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1341044 Alyref "Aly/REF export factor" [Mus musculus (taxid:10090)]

 Score = 292 (107.8 bits), Expect = 1.8e-29, Sum P(2) = 1.8e-29
 Identities = 56/103 (54%), Positives = 79/103 (76%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:    96 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 155

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
             ADA+ A+K+YN V LDG+PM I++V + I T+   PA ++N G
Sbjct:   156 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQRR-PAQSINRG 197

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=TAS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0006810 "transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

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

UNIPROTKB|E1C2L5 THOC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 285 (105.4 bits), Expect = 2.3e-29, Sum P(2) = 2.3e-29
 Identities = 56/108 (51%), Positives = 79/108 (73%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:    95 GAGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 154

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGV 122
             ADA+ A+K+YN V LDG+PM I++V + I T+   PA   +  N  G+
Sbjct:   155 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQRR-PAQRNHSVNRGGM 201

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

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

UNIPROTKB|E9PB61 ALYREF "THO complex subunit 4" [Homo sapiens (taxid:9606)]

 Score = 288 (106.4 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 56/103 (54%), Positives = 78/103 (75%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:   104 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 163

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
             ADA+ A+K+YN V LDG+PM I++V + I  +   PA +VN G
Sbjct:   164 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDAQRR-PAQSVNRG 205

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q86V81 ALYREF "THO complex subunit 4" [Homo sapiens (taxid:9606)]

 Score = 288 (106.4 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 56/103 (54%), Positives = 78/103 (75%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:    97 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 156

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
             ADA+ A+K+YN V LDG+PM I++V + I  +   PA +VN G
Sbjct:   157 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDAQRR-PAQSVNRG 198

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0000346 "transcription export complex" evidence=IDA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IDA

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-070928-29 alyref "Aly/REF export factor" [Danio rerio (taxid:7955)]

 Score = 288 (106.4 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 54/103 (52%), Positives = 76/103 (73%)

Query:    15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
             G  + +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+
Sbjct:   116 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 175

Query:    75 ADAVAAVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFG 117
             ADA+ A+K+YN V LDG+PM I++V + I  +   P   +N G
Sbjct:   176 ADALKAMKQYNGVPLDGRPMNIQLVTSQIDAQRRTPMQGLNRG 218

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00024369001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (243 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00000354001	SubName- Full=Chromosome chr9 scaffold_104, whole genome shotgun sequence; (434 aa)					•	•			0.812
	GSVIVG00026309001	SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (121 aa)						•			0.800
	GSVIVG00014829001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (812 aa)						•			0.800
	GSVIVG00028848001	SubName- Full=Chromosome chr1 scaffold_46, whole genome shotgun sequence; (176 aa)			•			•			0.633
	GSVIVG00034829001	SubName- Full=Chromosome chr4 scaffold_73, whole genome shotgun sequence; (202 aa)			•		•	•	•		0.599
	GSVIVG00037180001	SubName- Full=Chromosome chr16 scaffold_86, whole genome shotgun sequence; (201 aa)			•	•		•			0.572
	GSVIVG00006250001	SubName- Full=Chromosome chr1 scaffold_166, whole genome shotgun sequence; (320 aa)						•	•		0.463
	GSVIVG00029068001	SubName- Full=Chromosome chr12 scaffold_47, whole genome shotgun sequence; (360 aa)			•			•			0.462
	GSVIVG00020879001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (427 aa)						•			0.448
	GSVIVG00014203001	SubName- Full=Chromosome chr16 scaffold_10, whole genome shotgun sequence; (151 aa)				•	•	•	•		0.436

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	184
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	3e-46
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-33
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	3e-24
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-19
smart00360	73	smart00360, RRM, RNA recognition motif	8e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-13
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-12
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	6e-12
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	7e-12
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-11
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-11
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	7e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-09
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	3e-09
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	5e-09
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	5e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	7e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	8e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-06
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	1e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	4e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	4e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	4e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	5e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	7e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	9e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-05
cd12506	75	cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition m	3e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	4e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	5e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	7e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	7e-05
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	7e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	8e-05
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	8e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-04
pfam13865	76	pfam13865, FoP_duplication, C-terminal duplication	1e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	2e-04
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	2e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	3e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	3e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	4e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	4e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	4e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	5e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-04
cd12733	75	cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-	6e-04
pfam05918	543	pfam05918, API5, Apoptosis inhibitory protein 5 (A	6e-04
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	7e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	8e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	8e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	9e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.001
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.001
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	0.001
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.001
pfam05918	543	pfam05918, API5, Apoptosis inhibitory protein 5 (A	0.002
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.002
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.002
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.002
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.002
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.002
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	0.002
PTZ00070	257	PTZ00070, PTZ00070, 40S ribosomal protein S2; Prov	0.002
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.002
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.003
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.003
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.003
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	0.004

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score =  145 bits (369), Expect = 3e-46
 Identities = 50/75 (66%), Positives = 66/75 (88%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          TKL +SNLD+GVS++DIKELF+E G LK+ ++HYDRSGRS GTA+VV+ RRADA+ A+K+
Sbjct: 1  TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 84 YNNVQLDGKPMKIEI 98
          YN V LDG+PMKI++
Sbjct: 61 YNGVPLDGRPMKIQL 75

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score =  112 bits (282), Expect = 5e-33
 Identities = 41/75 (54%), Positives = 61/75 (81%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T+L +SNL Y V+ ED++ELF  VG++K+  I+YDRSGRS+GTA+VV+ +R DA  A+K+
Sbjct: 1  TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 84 YNNVQLDGKPMKIEI 98
          +N V LDG+PM++E+
Sbjct: 61 FNGVLLDGQPMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 90.0 bits (224), Expect = 3e-24
 Identities = 35/75 (46%), Positives = 49/75 (65%), Gaps = 6/75 (8%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T+L +SNL   V+ +DI ELFS +G LKR  +         G AEVVY R+ DA+ A+ +
Sbjct: 1  TRLVVSNLHPSVTEDDIVELFSAIGALKRARL------VRPGVAEVVYVRKDDALTAIDK 54

Query: 84 YNNVQLDGKPMKIEI 98
          YNN +LDG+PMK ++
Sbjct: 55 YNNRELDGQPMKCKL 69

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

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

 Score = 77.0 bits (190), Expect = 3e-19
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ NL    + ED++ELFS+ G+++   I  D+ G+SKG A V +    DA  A++  N
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 86 NVQLDGKPMKIE 97
            +LDG+ +K+ 
Sbjct: 61 GKELDGRKLKVS 72

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

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

 Score = 73.4 bits (181), Expect = 8e-18
 Identities = 25/73 (34%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
           L++ NL    + E+++ELFS+ G ++   +  D+ +G+SKG A V +    DA  A++ 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 84 YNNVQLDGKPMKI 96
           N  +LDG+P+K+
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 68.0 bits (167), Expect = 9e-16
 Identities = 25/70 (35%), Positives = 41/70 (58%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ NL    + ED+K+LFS+ G ++   I  D +GRSKG A V +    DA  A++  N
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 86 NVQLDGKPMK 95
            +L G+ ++
Sbjct: 61 GKELGGRELR 70

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

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

 Score = 66.1 bits (160), Expect = 3e-13
 Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 1/98 (1%)

Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
             L++ NL Y V+ ED++ELF + G +KR  +  DR +G+S+G A V +     A  A++
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 83  RYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSN 120
             N  +L+G+P++++        R+             
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKK 213

Length = 306

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

 Score = 60.5 bits (147), Expect = 1e-12
 Identities = 23/74 (31%), Positives = 43/74 (58%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL++S L + V+ E++++LF + G +K   +  +RSG+ KG A V Y   + A  AV + 
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 85 NNVQLDGKPMKIEI 98
          +  ++  K + + I
Sbjct: 64 DGTEIKEKTISVAI 77

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

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

 Score = 58.3 bits (142), Expect = 4e-12
 Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          LY+ NL   V+ ED++E FS  G ++   +  ++  R +G A V ++   DA AA+K+ N
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 86 NVQLDGKP 93
           + LDG+ 
Sbjct: 60 GLVLDGRT 67

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

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 58.2 bits (141), Expect = 6e-12
 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 2/77 (2%)

Query: 25 KLYISNLDYGVSNEDIKELF-SEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          K+ +SNL   V+   I+E F S++G +KR  + Y+  G+S G A + + R  DA  A  +
Sbjct: 1  KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 84 YNNVQLDGK-PMKIEIV 99
          +N    DG   MK+E+V
Sbjct: 61 FNGRIDDGNRKMKVEVV 77

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 58.1 bits (141), Expect = 7e-12
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR-SKGTAEVVYSRRADAVAAVKRY 84
          +Y+SNL + ++N D+ ++FS+ G + + +I  D+  R SKG A +++  R DA   VK  
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 85 NNVQLDGKPMKIEI 98
          NN +L G+ +K  I
Sbjct: 64 NNKELFGRTLKCSI 77

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 57.7 bits (140), Expect = 1e-11
 Identities = 23/71 (32%), Positives = 44/71 (61%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          +++ NL + V+ +D+K+LF E G++ R  +  D  GRSKG   V++    DA  A++ +N
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 86 NVQLDGKPMKI 96
             L+G+ +++
Sbjct: 61 GYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 23/73 (31%), Positives = 43/73 (58%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++++NLDY V  + +KE+F   G + R  I  D+ G+S+G   V +    +AV A+  +N
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 86 NVQLDGKPMKIEI 98
             L  +PM++++
Sbjct: 61 GQMLFDRPMRVKM 73

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 56.9 bits (138), Expect = 2e-11
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L++ NL Y  ++E ++E FSEVG +KR  +  D+ S + +G   V ++   DA  A++  
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 85 NNVQLDGKPMKIEI 98
             +  G+ + +E 
Sbjct: 62 KKTKFGGRKIHVEF 75

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

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

 Score = 55.7 bits (135), Expect = 6e-11
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
           LY+ NL Y V+ ED+K+LF + G++    +  DR +GRS+G   V      +A AA+++
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 84 YNNVQLDGKPMKI 96
           N     G+ + +
Sbjct: 61 LNGTDFGGRTLTV 73

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

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 55.4 bits (134), Expect = 7e-11
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYS--------IHYDRSGRSKGTAEVVYSRRADA 77
          +YIS L   V+ + + ELF  +G +KR          I+ D+    KG A V Y   + A
Sbjct: 1  IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 78 VAAVKRYNNVQLDGKPMKIE 97
           AA++ +N  +  G  +K+ 
Sbjct: 61 QAAIEWFNGYEFRGNKIKVS 80

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 54.9 bits (133), Expect = 1e-10
 Identities = 23/77 (29%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAV 81
          G KL++S L    + ++++ LFS+ G ++   +  D  +G S+G   V +    DA AA+
Sbjct: 1  GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 82 KRYNNVQLDGKPMKIEI 98
          +  N  +L+G+ +K+E 
Sbjct: 61 RDLNGKELEGRVIKVEK 77

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

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

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 21/72 (29%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRY 84
          LY+ NL + ++ +D++ +F   G+++   +  D  +GRSKG   + ++   DA  A+++ 
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 85 NNVQLDGKPMKI 96
          N  +L G+P+K+
Sbjct: 61 NGFELAGRPIKV 72

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

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

 Score = 58.3 bits (141), Expect = 2e-10
 Identities = 27/76 (35%), Positives = 42/76 (55%)

Query: 23  GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
           G  LY+ NLD  V++E ++ELFSE G++    +  D  G S+G   V +S   +A  AV 
Sbjct: 285 GVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344

Query: 83  RYNNVQLDGKPMKIEI 98
             +   L GKP+ + +
Sbjct: 345 EMHGRMLGGKPLYVAL 360

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

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

 Score = 52.6 bits (127), Expect = 8e-10
 Identities = 25/79 (31%), Positives = 46/79 (58%), Gaps = 6/79 (7%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          ++I NL +  + E++KELFS+ G++K   I  D+ +G SKGTA V +  +  A   ++  
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 85 NN-----VQLDGKPMKIEI 98
          +N     + LDG+ + + +
Sbjct: 63 DNAEDSGLSLDGRRLIVTL 81

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 52.2 bits (126), Expect = 1e-09
 Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 27 YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++ N+ Y  + E + E+FSEVG +  + +  DR +G+ KG     +     A +A++  N
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 86 NVQLDGKPMKIE 97
            + +G+ ++++
Sbjct: 62 GYEFNGRALRVD 73

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

>gnl|CDD|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 = 51.9 bits (125), Expect = 1e-09
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVAAVKR 83
          +L++ NL +  + E+++ELF   G++    +  D+   RSKG A V +     AV A   
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 84 YNNVQLDGK 92
           +     G+
Sbjct: 61 LDGSIFQGR 69

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

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 37/72 (51%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
          G  LY+ NLD  + +E ++E FS  G +    +  D  GRSKG   V +S   +A  AV 
Sbjct: 1  GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

Query: 83 RYNNVQLDGKPM 94
            N   + GKP+
Sbjct: 61 EMNGRIIGGKPL 72

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

 Score = 51.4 bits (124), Expect = 2e-09
 Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSK-GTAEVVYSRRADAVAAVKRY 84
          LY+ NL +  + E I ELFS  GD+KR  +  DR  ++  G   V Y  R DA  AVK  
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 85 NNVQLDGKPMKIE 97
          N  +LD + ++++
Sbjct: 61 NGTKLDDRIIRVD 73

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

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 51.2 bits (122), Expect = 3e-09
 Identities = 24/73 (32%), Positives = 45/73 (61%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++++NLD+ V  + +KE+FS  G +KR  I  D+ G+S+G   V + +  +AV A+  +N
Sbjct: 3  IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 86 NVQLDGKPMKIEI 98
             L  +PM +++
Sbjct: 63 GQFLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 50.4 bits (120), Expect = 5e-09
 Identities = 24/75 (32%), Positives = 45/75 (60%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          + ++++NLDY V  + +KE+FS  G + R  I  D+ G+S+G   V + +  +AV A+  
Sbjct: 1  STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60

Query: 84 YNNVQLDGKPMKIEI 98
          +N   L  +PM +++
Sbjct: 61 FNGQLLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 49.9 bits (120), Expect = 8e-09
 Identities = 23/69 (33%), Positives = 39/69 (56%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          +L + NL +  +  D+K+LFS  G +   +I     G+ KG A V ++ +ADA  A+K  
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 85 NNVQLDGKP 93
          N  ++ G+P
Sbjct: 61 NGKKIKGRP 69

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

 Score = 49.6 bits (119), Expect = 8e-09
 Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          +++SNLDY V  +++++LFS+ G++    +  +  G+SKG A V +        A+K  +
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL-D 60

Query: 86 NVQLDGKPM 94
             + G+PM
Sbjct: 61 RELIKGRPM 69

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

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

 Score = 49.5 bits (119), Expect = 1e-08
 Identities = 22/71 (30%), Positives = 37/71 (52%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T +Y+ NL   + +E +KELF + G +    +  D  G+SKG   V +     A  AV+ 
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 84 YNNVQLDGKPM 94
           N  +++GK +
Sbjct: 62 LNGKEVNGKKL 72

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

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 7/76 (9%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVA 79
          ETG +L++ NL Y    +D+++LFS+ G+L    +  D +SG+SKG A V++    D   
Sbjct: 1  ETG-RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF---LDPED 56

Query: 80 AVKRYNNVQLDGKPMK 95
          AVK Y   +LDGK  +
Sbjct: 57 AVKAYK--ELDGKVFQ 70

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|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 = 49.1 bits (118), Expect = 2e-08
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVAAVKR 83
          KL++  L    + ED++ LF E G+++  +I  D+  G+SKG A V +S R +A  A++ 
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 84 YNN 86
           + 
Sbjct: 61 LHG 63

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 19/78 (24%), Positives = 43/78 (55%), Gaps = 5/78 (6%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSI---HYDRSGRS-KGTAEVVYSRRADAVAA 80
          ++Y+ NLD+ +  +D++ +FS+ G+++   I     ++ GR   G A V +   + A  A
Sbjct: 2  EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 81 VKRYNNVQLDGKPMKIEI 98
          ++  N  +L G+ + + +
Sbjct: 62 LQ-LNGTELGGRKISVSL 78

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

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

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ NL +    +D++E F E G++    I  D  GRSKG   V ++    A  A+++  
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSG 61

Query: 86 NVQLDGKPMKIEI 98
            +L G+ +++++
Sbjct: 62 E-ELLGREIRVDL 73

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

 Score = 47.6 bits (114), Expect = 5e-08
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          +Y+ NLD  V+ E + ELF + G +    I  DR +   +G   V +    DA  A+K  
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 85 NNVQLDGKPMKI 96
          N ++L GKP+++
Sbjct: 61 NMIKLYGKPIRV 72

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

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

 Score = 51.1 bits (122), Expect = 7e-08
 Identities = 30/124 (24%), Positives = 59/124 (47%), Gaps = 2/124 (1%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKR 83
           KLY+ NL + ++ ++++++F   GD++   +H D  +GRSKG   + +    +A  A++ 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 84  YNNVQLDGKPMKIEIVGTNIATRTAAPA-ANVNFGNSNGVPRGGQGRGGAFRRLRGGGGG 142
            N  +L G+P+K+     +     AA    +++     G     + R     +L    G 
Sbjct: 248 MNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGD 307

Query: 143 GGRG 146
           GG  
Sbjct: 308 GGLL 311

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

 Score = 47.0 bits (112), Expect = 9e-08
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
           L++ NL + V +E +K  F + G +    +  DR +GRS+G   V +    DA  A++ 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 84 YNNVQLDGKPMKIE 97
           +  +LDG+P+ ++
Sbjct: 61 MDGKELDGRPINVD 74

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

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

 Score = 46.4 bits (111), Expect = 1e-07
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 40 IKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI 98
          + +LFS  G++++  +      +  G A V +S    A  AV+  N V   G+P++++ 
Sbjct: 1  LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 46.5 bits (111), Expect = 1e-07
 Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 27 YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++ N+DYG + E+++E F   G + R +I  D+ +G+ KG A + +     +V      N
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFL-DKSSVENALLLN 61

Query: 86 NVQLDGKPMKI 96
            +  G+ +K+
Sbjct: 62 ESEFRGRQIKV 72

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

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 46.4 bits (111), Expect = 2e-07
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSI--HYDRSGR----SKGTAEVVYSRRADA 77
          T L++ NL++  + E +K+ F + G ++  +I    D  G     S G   V +  +  A
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 78 VAAVKRYNNVQLDGKPMKIEI 98
            A+KR     LDG  +++++
Sbjct: 61 QKALKRLQGTVLDGHALELKL 81

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 19/70 (27%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
          TK+++  L Y  +++ +++ FS+ G+++   +  DR +G+S+G   V +  +  A  A K
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 83 RYNNVQLDGK 92
            N + +DG+
Sbjct: 61 DPNPI-IDGR 69

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 30  NLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRYNNVQ 88
            L    +  D++E+FS  G +++  + YD ++GRS+G   V +    DA  A +R N ++
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 89  LDGKPMKIEIVGT 101
           +DG+ ++++   T
Sbjct: 66  IDGRRIRVDYSIT 78

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

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

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 39/72 (54%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ NLD  V+ E + ELF + G L+   I  D +G+ K  A V +        A++  N
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 86 NVQLDGKPMKIE 97
           ++L G+ ++I+
Sbjct: 64 GIRLFGRELRIK 75

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

>gnl|CDD|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 = 45.4 bits (108), Expect = 4e-07
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYS-IHYDRSGRSKGTAEVVYSRRADAVAAVK 82
          T L+I +L   V+ ED+K LF E G+++    I        +G A V    R DA  A++
Sbjct: 3  TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQ 56

Query: 83 RYNNVQLDGKPMKI 96
          +  NV+L GK +K+
Sbjct: 57 KLRNVKLAGKKIKV 70

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

 Score = 48.3 bits (115), Expect = 5e-07
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 1/99 (1%)

Query: 3   ADQVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR 62
              V  F  +    A+ ++  T LY+ NLD  V+ + ++ELF++ G++   ++  D SGR
Sbjct: 158 EVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGR 217

Query: 63  SKGTAEVVYSRRADAVAAVKRYNNVQLDG-KPMKIEIVG 100
           S+G A V + +  DA  AV+  N  ++   K  K   VG
Sbjct: 218 SRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVG 256

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

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

 Score = 44.7 bits (106), Expect = 6e-07
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L++ NL +    + I E F E G++    +  D  SGR KG   V +S +  A AA+   
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 85 NNVQLDGKPMKIE 97
              L G+P++++
Sbjct: 61 GGTDLLGRPVRLD 73

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

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 44.8 bits (107), Expect = 7e-07
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 26 LYISNLDYGVSNEDIK----ELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAV 81
          LYI+NL+  +  +++K     LFS+ G      I   ++ + +G A VV+     A  A+
Sbjct: 2  LYINNLNEKIKKDELKRSLYALFSQFG--PVLDIVASKTLKMRGQAFVVFKDVESATNAL 59

Query: 82 KRYNNVQLDGKPMKIE 97
          +         KPM+I+
Sbjct: 60 RALQGFPFYDKPMRIQ 75

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 44.6 bits (106), Expect = 7e-07
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          LY+ NLD  V+ + + ELFS++G +K   +  +         E  Y     A AA++  N
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVE--YYDHRSAAAALQTMN 58

Query: 86 NVQLDGKPMKI 96
             + G+ +K+
Sbjct: 59 GRLILGQEIKV 69

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

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

 Score = 44.5 bits (106), Expect = 8e-07
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 28 ISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++NL      +D++ELF   G + R  +  D+ +G+S+G A V +  R DA  A+++ N
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 62

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 44.1 bits (104), Expect = 1e-06
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRY 84
          L++ NL + V+ ED+ + FS+V  +K   +  D  +G S+G   V ++   DA  A+ + 
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 85 NNVQLDGKPMKIEI 98
           N +L G+ ++++I
Sbjct: 62 KNKKLHGRILRLDI 75

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

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

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 9/82 (10%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYS--------IHYDR-SGRSKGTAEVVYSRRAD 76
          +++SNL    + +D+ E F  +G +K           ++ D+ +G  KG A V Y     
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 77 AVAAVKRYNNVQLDGKPMKIEI 98
          A AA++ +NN    G  +K+ +
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSL 82

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

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

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 17/64 (26%), Positives = 38/64 (59%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL++  L    +  D++ +F+  G ++  ++  D++G+S+G A V ++ R  A+ A+K  
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62

Query: 85 NNVQ 88
          ++ Q
Sbjct: 63 HHSQ 66

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

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVAAVK 82
          T LY++NL   ++ ++++++F   G++ + ++  D+S G  +G A V Y +R +A AA+ 
Sbjct: 1  TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 83 RYNNVQLDGKPMKIEI 98
            N     G  M + +
Sbjct: 61 SLNGTIPPGSTMPLSV 76

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

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

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 38/72 (52%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ NLD  V+ E I ELF + G + +  I  D+ G+ K  A V +        A+   N
Sbjct: 4  LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 86 NVQLDGKPMKIE 97
           ++L G+P+ I+
Sbjct: 64 GIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 43.3 bits (103), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
          G ++++  +   +  +++  LF + G +    +  D SG ++G A V Y+ +  A  AVK
Sbjct: 1  GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVK 60

Query: 83 RYNNVQLD-GKPMKIEI 98
          + +N ++  GK + + I
Sbjct: 61 QLHNYEIRPGKRLGVCI 77

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 43.0 bits (102), Expect = 3e-06
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          LY+ NL + +S+E++ +LF + G +    I    +  ++GTA VVY    DA  A    +
Sbjct: 5  LYVRNLPFKISSEELYDLFGKYGAI--RQIRIGNTKETRGTAFVVYEDIYDAKNACDHLS 62

Query: 86 NVQLDGK 92
             +  +
Sbjct: 63 GFNVANR 69

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

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          ++++ +      ED+ + F+E G++K   ++ DR +G  KG A + Y  + +A AA++  
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 85 NNVQLDGKPMKI 96
          N  +L G+ + +
Sbjct: 69 NGKELLGQTISV 80

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

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

 Score = 42.9 bits (102), Expect = 3e-06
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L++  L   V+ + +KE+FS  G +K   +  DR     +G A V +    DA  A+K  
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 85 NNVQLDGKPMKIE 97
          +  Q+DG+ + +E
Sbjct: 61 DGGQIDGQEVTVE 73

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

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

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
          T L ++ L   ++ ++I+ LFS +G+++   +  D+ +G+S G   V Y    DA  A+ 
Sbjct: 2  TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 83 RYNNVQLDGKPMKI 96
            N ++L  K +K+
Sbjct: 62 TLNGLRLQNKTIKV 75

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 43.1 bits (102), Expect = 4e-06
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDL----KRYSIHYDRSGRSK--GTAEVVYSRRADAV 78
          ++YISNL Y  S ED++E   +   +       ++   RS R +  G A   +S    A 
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 79 AAVKRYNNVQLDGKPMKI 96
            VK  N      + + +
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 43.0 bits (102), Expect = 4e-06
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS----GRSKGTAEVVYSRRADAVA 79
          T LY+ NL+  V+ E + + F   G L    I + R+     R++    V +  RADA  
Sbjct: 2  TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 80 AVKRYNNVQLDGKPMKI 96
          A+   +   + G  +K+
Sbjct: 62 ALDELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 21/73 (28%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          +++ N+ Y  + E +K++FSEVG +  + + YDR +G+ KG     Y  +  A++A++  
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 85 NNVQLDGKPMKIE 97
          N  +L+G+ ++++
Sbjct: 61 NGYELNGRQLRVD 73

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

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 42.7 bits (101), Expect = 4e-06
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          L + NL   VSNE +++ FS+ G+++R  +  D  GRS G   V +SR+  A AA+KR
Sbjct: 2  LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 42.6 bits (100), Expect = 4e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ NL+  V  E + ELF + G L + +I  D+ G+ K    V +        A+   N
Sbjct: 4  LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 86 NVQLDGKPMKI 96
           ++L G+P+K+
Sbjct: 64 GIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 42.6 bits (100), Expect = 4e-06
 Identities = 22/63 (34%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 36 SNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM 94
          +  D++E+FS  G L   ++ YD R+GRS+G A V + R  D+  A++  N ++LDG+ +
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71

Query: 95 KIE 97
          +++
Sbjct: 72 RVD 74

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

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

 Score = 42.3 bits (100), Expect = 5e-06
 Identities = 19/75 (25%), Positives = 38/75 (50%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          ++L + NL  G+  + +++LF   G +    + Y + G+ +    V Y    +A  A+K 
Sbjct: 1  SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 84 YNNVQLDGKPMKIEI 98
          +NN  +D   + +EI
Sbjct: 61 FNNSFIDTSKITVEI 75

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 42.2 bits (100), Expect = 7e-06
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIH--YDRSGRSKGTAEVVYSRRADAVAAVKR 83
          + +  L +  + EDI++ FS + D+    IH  YD  GR  G A V ++   DA  A+++
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGL-DIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60

Query: 84 YNN 86
          +NN
Sbjct: 61 HNN 63

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 43.5 bits (102), Expect = 7e-06
 Identities = 39/126 (30%), Positives = 63/126 (50%), Gaps = 18/126 (14%)

Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
           TKL+I  L +G  +  +++ F+  GD+    +  DR +GRS+G   V ++    A AA+ 
Sbjct: 35  TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94

Query: 83  RYNNVQLDGKPMKIEIVGTNIAT-RTAAPAANVNFGNSNGVPRGGQGRGGAFRRLRGGGG 141
             +  +L+G+ +++     N A  R +AP        + G   G  G GG +    GGGG
Sbjct: 95  EMDGKELNGRHIRV-----NPANDRPSAP-------RAYGGGGGYSGGGGGY----GGGG 138

Query: 142 GGGRGF 147
            GG GF
Sbjct: 139 DGGGGF 144

Length = 144

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

 Score = 41.9 bits (98), Expect = 9e-06
 Identities = 23/63 (36%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 36 SNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM 94
          +  D++E+FS+ G +   SI YD+ S RS+G A V +    DA  A +R N ++LDG+ +
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81

Query: 95 KIE 97
          +++
Sbjct: 82 RVD 84

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

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

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
          KL++ NL + V ++++KE FS+ G +K  ++ +D+ +G SKG   V +S R D +    +
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR-DGLENALQ 59

Query: 84 YNNVQLDGKPMKI 96
               L+G  +++
Sbjct: 60 KQKHILEGNKLQV 72

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

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

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 19/79 (24%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGD------LKRYSIHYDRSGRSKGTAEVVYSRRADAV 78
          KL++ NL    ++E+++ LF + G       +K Y               V      DA 
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNY-------------GFVHMEEEEDAE 47

Query: 79 AAVKRYNNVQLDGKPMKIE 97
           A+K  N  +  GK + +E
Sbjct: 48 DAIKALNGYEFMGKRINVE 66

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

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

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L + NL Y  + +D++ +F + G++    I  DR +  S+G A V +  + DA  A+   
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 85 NNVQLDGKPMKI 96
          +  +LDG+ +++
Sbjct: 61 DGKELDGRELRV 72

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

>gnl|CDD|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 = 40.7 bits (96), Expect = 2e-05
 Identities = 19/74 (25%), Positives = 39/74 (52%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          TKL + N+ +  + ++++ELFS  G +K   +     G  +G A V +  + +A  A++ 
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 84 YNNVQLDGKPMKIE 97
            +  L G+ + +E
Sbjct: 61 LKSTHLYGRHLVLE 74

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          L + NL    ++E  +EL S  G ++R + ++ + +G SKG   V Y+ +A A+ A K  
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA-KN- 59

Query: 85 NNVQLDGKPMKI 96
             QLDGK +  
Sbjct: 60 ---QLDGKQIGG 68

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 27 YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++  L   V   D+ E FS+ G ++   I  DR S RSKG A V +        A+    
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LT 61

Query: 86 NVQLDGKPMKI 96
            +L G+P+ +
Sbjct: 62 GQRLLGQPIMV 72

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

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

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 7/72 (9%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          E+G +L+I NL Y  + ED+++LFS+ G L    +  D+ + + KG A V Y     AV 
Sbjct: 1  ESG-RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVK 59

Query: 80 AVKRYNNVQLDG 91
          A   +   +LDG
Sbjct: 60 A---FA--ELDG 66

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

>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 31 LDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          L Y  +  DI E FS +  +    I Y+  GR+ G A+V ++   DAVAA+ +
Sbjct: 8  LPYRATENDIFEFFSPLNPV-NVRIEYNADGRATGEADVEFATHEDAVAAMSK 59

This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

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

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
            LY+S L   ++ +++++LFS+ G +    I  D+ +G S+G   + + +R +A  A+K
Sbjct: 1  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 83 RYNNVQLDG 91
            N  + +G
Sbjct: 61 GLNGQKPEG 69

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

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

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR---SGRSKGTAEVVYSRRADAVAAVK 82
          LY+ +L   V+   + E+FS  G +   SI   R   + RS G A V +   ADA  A+ 
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVL--SIRVCRDLITRRSLGYAYVNFQNPADAERALD 59

Query: 83 RYNNVQLDGKPMKI 96
            N   + GKP++I
Sbjct: 60 TLNFDVIKGKPIRI 73

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

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

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRY 84
          +YI +L +G   +++K+ FS+ G +K   +    ++G SK    + +     A  A K  
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 85 NNVQLDGKPMKIEIV 99
          NN  L GK +++ ++
Sbjct: 62 NNYLLMGKVLQVHVL 76

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

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

 Score = 42.7 bits (100), Expect = 4e-05
 Identities = 26/111 (23%), Positives = 56/111 (50%), Gaps = 3/111 (2%)

Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
           T LY++NL   ++++ +  +F + G + + +I  D+ +G  +G A V +++R +A  A+ 
Sbjct: 194 TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS 253

Query: 83  RYNNVQLDG--KPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRGG 131
             NNV  +G  +P+ + +   +   +     + +  GN   +  G  G  G
Sbjct: 254 ALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGHGNMGMAG 304

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

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 3/75 (4%)

Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
           L++ NL Y ++ +++KE+F +  D++   +   + G SKG A + +   A+A  A++   
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDIR---LPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 86  NVQLDGKPMKIEIVG 100
             ++DG+ + ++  G
Sbjct: 63  GAEVDGRSIVVDYTG 77

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

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

 Score = 40.0 bits (94), Expect = 4e-05
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSI-HYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          +Y+  L    ++E +K +FS+ G +   S+  Y  +G  KG A + +    +A  A K  
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 85 NN 86
          NN
Sbjct: 62 NN 63

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
           +YI  L Y ++  DI  +FS+ G++   ++  D+ +G+SKG A + Y  +   + AV   
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 85  NNVQLDGKPMKIEIVG 100
           N ++L G+ ++++ V 
Sbjct: 72  NGIKLLGRTIRVDHVR 87

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 25 KLYISNLDYGVSNEDIKELFS---EVGDLKRYSIHYD--RSGRSKGTAEVVYSRRADAVA 79
          +LY+ NL   V+ ED+  +F    +    ++          GR KG A V +     A  
Sbjct: 3  RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 80 AVKRYNNVQLDGKPMKIE 97
          A+   N   L GKPM I+
Sbjct: 63 ALNLVNGYVLKGKPMVIQ 80

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 40 IKELFSEVGDLKRYSIHY--DRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD 90
          ++++FS+ G  K   I+   D +G++KG A V ++   +A  AVK  N  +LD
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

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

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
          K++I  L   +S + +KEL    G LK +++  D  +G SKG A   Y   +    A+  
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 84 YNNVQLDGK 92
           N +QL  K
Sbjct: 62 LNGMQLGDK 70

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 24 TKLYISNLDYGVSNEDIKELFS----EVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVA 79
          ++L + NL   ++  ++KE FS    E+ D+K   +     G+S+  A + Y    +A  
Sbjct: 1  SRLIVKNLPASLTEAELKEHFSKHGGEITDVK---LLRTEDGKSRRIAFIGYKTEEEAQK 57

Query: 80 AVKRYNNVQLDGKPMKIE 97
          A   +NN  ++   + +E
Sbjct: 58 AKDYFNNTYINTSKISVE 75

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 39.5 bits (93), Expect = 5e-05
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
          GT L + NLD  +S+++++ LFS+ G++K   I       S+   E    R   A AA+ 
Sbjct: 2  GT-LLVFNLDSPISDQELRSLFSQFGEVK--DIRETPLRPSQKFVEFYDIR--AAEAALD 56

Query: 83 RYNNVQLDGKPMKIE 97
            N     G  +K++
Sbjct: 57 ALNGRPFLGGRLKVK 71

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

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

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVAAVKRY 84
          LY+S L   ++ ++++ LFS  G +    I  D   G S+G   + + +R +A  A+K  
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 85 NNVQLDG 91
          N     G
Sbjct: 63 NGTIPPG 69

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

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

 Score = 39.9 bits (94), Expect = 5e-05
 Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L+++ L+Y  +   ++  F E G +KR  +  D+ +G+ +G A + +    D  AA K  
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 85 NNVQLDGK 92
          +  ++DG+
Sbjct: 64 DGKKIDGR 71

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

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

 Score = 42.2 bits (99), Expect = 6e-05
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVA 79
          E+ T L ++ L   ++ E+I+ LF+ +G+++   +  D+  G+S G   V Y R  DA  
Sbjct: 1  ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 80 AVKRYNNVQLDGKPMKIEI 98
          AV   N ++L  K +K+  
Sbjct: 61 AVNSLNGLRLQNKTIKVSY 79

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

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

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          LY+ NL    + E ++ELFSE G+++R     D        A V +  R DAV A++  N
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 86 NVQLDGKPMKI 96
            +L+G P+++
Sbjct: 57 GKELEGSPIEV 67

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

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 42.2 bits (99), Expect = 6e-05
 Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
           ++YI NL   +  + IKEL    GDLK +++  D  +G SKG A   Y   +    A+  
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356

Query: 84  YNNVQLDGKPMKIE--IVGTNIAT 105
            N        + ++   VG N AT
Sbjct: 357 LNGKDTGDNKLHVQRACVGANQAT 380

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGT----AEVVYSRRADAVAA 80
          +L+I NLD  ++   + +LFS+ G +K++   + +SG  KG       V +  + +A  A
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 81 VKRYNNVQLDGK 92
          +K  N     GK
Sbjct: 61 LKSLNGKTALGK 72

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 39.2 bits (92), Expect = 7e-05
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 26 LYISNLDYGVSNEDIKELFSEVG--DLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
          LY+ NL +  ++ED++   +E G  D+K       + +G+SKG A V ++  A A A  +
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 83 RYNNVQLDGKPM 94
          +    + +GK  
Sbjct: 61 KLEGREFNGKKC 72

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 23/40 (57%), Positives = 23/40 (57%)

Query: 115 NFGNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRG 154
            FG   G  RGG G GG     RGGG GGGRG GRG G G
Sbjct: 5   GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGG 44

Length = 293

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 16/72 (22%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 28 ISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRYNN 86
           SNL+  +    +K++  + G+++   I++  ++ +  G A VV+     A   V++ N 
Sbjct: 7  FSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQ 66

Query: 87 VQLDGKPMKIEI 98
            + GK +K+ +
Sbjct: 67 TSVMGKIIKVFL 78

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 41.6 bits (98), Expect = 8e-05
 Identities = 22/43 (51%), Positives = 22/43 (51%)

Query: 115 NFGNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRER 157
             G   G  RGG   GG      GGG GGGRG GRGRGRG   
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGG 43

Length = 293

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 39.2 bits (91), Expect = 8e-05
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSE-VGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          + +ISN+ + V  + +K+L  E VG++    +  D  G+S+G A V +        AV+ 
Sbjct: 1  RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60

Query: 84 YNNVQLDGKPMKIE 97
           N   L+G+P+K++
Sbjct: 61 LNKHVLNGRPLKVK 74

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYS-IHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          +++  L   V+ E++ E FS  G +   + I   R+  +   A + + R   A  AV+  
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIK--RANHTNAFAFIKFEREQAAARAVESE 63

Query: 85 NNVQLDGKPMKIE 97
          N+  L  K M ++
Sbjct: 64 NHSMLKNKTMHVQ 76

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

>gnl|CDD|222425 pfam13865, FoP_duplication, C-terminal duplication domain of Friend of PRMT1

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 123 PRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGR---ERNEKISAEDLDADLDKYYS 175
             G +G  G   R RG G   GR  GRG  +G+    + +  + EDLDA+LD+Y S
Sbjct: 1   SGGRKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPKPKTREDLDAELDQYMS 56

Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localised to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it colocalises with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation. Length = 76

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
           KL+I  L +  + + ++++FS+ G +    +  DR + RS+G   V +    DA  A+  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 84  YNNVQLDGKPMKIEIVG 100
            N   +DG+ ++++  G
Sbjct: 62  MNGKSVDGRQIRVDQAG 78

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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVAAV 81
             L++ NL Y  + E +   FS+ G ++      D+S GR+KGT  V +  +    A +
Sbjct: 1  DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 82 K 82
          K
Sbjct: 61 K 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLK--RYSIHYDRSGRSKGTAEVVYSRRADAVAAV 81
          TK+ + NL +  + +D++ LFS  G LK  R    +D+S R     E   ++  +A+ A+
Sbjct: 1  TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAK--EALNAM 58

Query: 82 KRYNNVQLDGKPMKIE 97
              +  L G+ + ++
Sbjct: 59 NALKDTHLLGRRLVLQ 74

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

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 25 KLYISNLDYGVSNEDIKELF-SEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          +++ISN+ Y +  +D+K+LF  +VG++    +  D  G+S+G   V +  +     A++ 
Sbjct: 1  RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 84 YNNVQLDGKPMKI 96
           N  +L G+ + +
Sbjct: 61 MNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 19/74 (25%), Positives = 41/74 (55%)

Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
             +++ NLD  V N+ + + FS+ G++    +  D +G+S+G   V + +   A AA+++
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148

Query: 84  YNNVQLDGKPMKIE 97
            N + L+ K + + 
Sbjct: 149 VNGMLLNDKEVYVG 162

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

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
           K+ ISN+   V  ED+  L S  G +K       +S  +  T  V Y     A  AV +
Sbjct: 1  RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETA--TVNVTYESPEQAQQAVNK 58

Query: 84 YNNVQLDGKPMKIE 97
           N  + +G  +K+ 
Sbjct: 59 LNGHEYEGSKLKVS 72

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 9/83 (10%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLK--------RYSIHYDRSGRSKGTAEVVYSRRA 75
          T +Y+S L   ++ E+  E+FS+ G +K        +  ++ D +G  KG A   Y +  
Sbjct: 2  TNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEE 61

Query: 76 DAVAAVKRYNNVQ-LDGKPMKIE 97
              A++  +  +   G  MK+E
Sbjct: 62 SVELAIQLLDGTEIGRGYKMKVE 84

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

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

 Score = 40.4 bits (94), Expect = 3e-04
 Identities = 42/188 (22%), Positives = 65/188 (34%), Gaps = 49/188 (26%)

Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
           LY+ NL    + E I++ FSE    K      +R  + +  A V +  R DAV A+   N
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGK-----VERVKKIRDYAFVHFEDREDAVKAMDELN 290

Query: 86  NVQLDGKPMKIEI--------------------------------VGTNIATRTAAPA-- 111
             +L+G  +++ +                                V    +   A     
Sbjct: 291 GKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYY 350

Query: 112 ANVNFGNSNGVPR-----GGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKISAEDL 166
            +  +  S   PR      G+GRGGA  R  GG G    G+    G     ++     + 
Sbjct: 351 YHPPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPYGYEAYYGDYYGYHDYRGKYE- 409

Query: 167 DADLDKYY 174
               DKYY
Sbjct: 410 ----DKYY 413

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRY 84
          LY+  L   V  + +   F   GD+K   I  D  + + +G A V +    DA AA+   
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 85 NNVQLDGKPMKI 96
          N  +L G+ +++
Sbjct: 61 NESELFGRTIRV 72

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

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

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 20/63 (31%), Positives = 36/63 (57%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL++  L+   + ++++E+FS  G ++   +  D   +S+G A V YS +  A AA+K  
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 85 NNV 87
          N V
Sbjct: 61 NGV 63

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L+I +L    +++D+ +LF+  G++    +  D+ +G+SK    V Y     A AA+K  
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 85 NNVQLDGKPMKIE 97
          N  Q+ GK +K++
Sbjct: 61 NGFQVGGKRLKVQ 73

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

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAV 81
          +Y+ N+DYG + E+++  FS  G + R +I  D+ SG  KG A + ++ R    AAV
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV 58

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T +Y+ NL +G++ E+++  FS  G     +I   R  + KG A V +     A  A+  
Sbjct: 1  TTVYVGNLPHGLTEEELQRTFSPFG-----AIEEVRVFKDKGYAFVRFDTHEAAATAIVA 55

Query: 84 YNNVQLDGKPMK 95
           N   ++G+ +K
Sbjct: 56 VNGTSINGQTVK 67

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

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
          T L ++ L   ++ E+++ LF  +G ++   I  DR +G+S G   V Y    DA  A+ 
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 83 RYNNVQLDGKPMKI 96
            N  ++  K +K+
Sbjct: 61 TLNGFEIRNKRLKV 74

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

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 37.2 bits (86), Expect = 4e-04
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYSRRADAVAAVKRY 84
          L ++NL Y  S + ++E+F      K  SI   ++ GR KG A V +    DA  A+   
Sbjct: 4  LVVNNLSYSASEDSLQEVFE-----KATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSC 58

Query: 85 NNVQLDGKPMKIE 97
          NN +++G+ +++E
Sbjct: 59 NNTEIEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIH-YDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          L++ NL +  + ++++  F  VG ++R  +  ++ SG+ KG A V +     A  A+K  
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK-- 58

Query: 85 NNVQLDGKPMKIEI 98
              L+G+ +++E 
Sbjct: 59 -GKHLNGRALRVEY 71

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L++ N++  V +E+++ LF + GD++  +++   + + +G   V Y     A  A +   
Sbjct: 4  LFVRNINSNVEDEELRALFEQFGDIR--TLYT--ACKHRGFIMVSYYDIRAARRAKRALQ 59

Query: 86 NVQLDGKPMKI 96
            +L G+ + I
Sbjct: 60 GTELGGRKLDI 70

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

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

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 27 YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++ NL + +  E++++ F + GD++   I  DR +G  KG   V++  +     A+K  N
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL-N 61

Query: 86 NVQLDGKPMKIE 97
           ++L G+ ++++
Sbjct: 62 GIKLKGRKIRVK 73

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          TKL++ N+    +N++++  F E G +    I        K  A V   R  DAV A++ 
Sbjct: 1  TKLHVGNISSSCTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEAIRG 53

Query: 84 YNNVQLDGKPMKIE 97
           +N +  GK M ++
Sbjct: 54 LDNTEFQGKRMHVQ 67

This subgroup corresponds to the RRM2 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|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 = 37.4 bits (87), Expect = 4e-04
 Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAA 80
           KL++  +   +  +D++ LF + G +   ++  D+ +G  KG A + Y  R  A+ A
Sbjct: 6  IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63

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

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          +YI +L +G    ++++ FS+ G + R       ++G+SKG A V +     A    +  
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 85 NNVQLDGKPMKIE 97
          NN  L  + +K +
Sbjct: 62 NNYLLFERLLKCK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L++ NL Y  + ED+   F   G      +  D+ +G+SKG A V +   A+A+    + 
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFD-TAEAMTKALKL 61

Query: 85 NNVQLDGKPMKIE 97
          ++  L G+ + +E
Sbjct: 62 HHTLLKGRKINVE 74

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 36.7 bits (85), Expect = 6e-04
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          +++  L +  S +DI   F+ +    R  I Y   GR+ G A+V +    DAVAA+ +
Sbjct: 3  VHMRGLPFQASGQDIVNFFAPLKPT-RILIEYSSDGRATGEADVHFESHDDAVAAMAK 59

This subgroup corresponds to the RRM3 of G-rich sequence factor 1 (GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5)

 Score = 39.3 bits (91), Expect = 6e-04
 Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 100 GTNIATRTAAPAANVNF---GNSNGVPRGGQGRGGAFR-RLRGGGGGGGRGFGRGRG 152
           G N+  + + P+ +       +  G+ + GQ  GG  R R RG GGGGGRG G  RG
Sbjct: 485 GNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRG 541

This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors. Length = 543

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.9 bits (86), Expect = 7e-04
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 27 YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN 86
          Y+ NLD   + + + E FS+ G++K Y        +    A V ++ +   + A+K  N 
Sbjct: 8  YVGNLDPTTTADQLLEFFSQAGEVK-YVRMAGDETQPTRYAFVEFAEQTSVINALK-LNG 65

Query: 87 VQLDGKPMKIE 97
              G+P+K+ 
Sbjct: 66 AMFGGRPLKVN 76

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 36.3 bits (84), Expect = 8e-04
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          L + NLD  VSN+D+ ++F   G++K   I    + R     E    R A+  AA+K  N
Sbjct: 4  LVVFNLDPSVSNDDLHQIFGAYGEIK--EIRETPNKRHHKFIEFYDVRSAE--AALKALN 59

Query: 86 NVQLDGKPMKIE 97
            ++ GK +K+E
Sbjct: 60 RSEIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.6 bits (84), Expect = 8e-04
 Identities = 21/58 (36%), Positives = 32/58 (55%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          L + NL   VSNE ++E FS+ G ++R  +  D  GRS G   V ++ +  A  A +R
Sbjct: 2  LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 36.6 bits (84), Expect = 9e-04
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          ++ T L ++ L   ++ E+ K LF  +G+++   +  D+ +G+S G   V Y    DA  
Sbjct: 1  DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 80 AVKRYNNVQLDGKPMKI 96
          A+   N ++L  K +K+
Sbjct: 61 AINTLNGLKLQTKTIKV 77

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 17/40 (42%), Positives = 17/40 (42%)

Query: 116 FGNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGR 155
            G   G   GG   GG     RGGG G GRG G G   G 
Sbjct: 10  RGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGG 49

Length = 293

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSE-VGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          +++ISN+ Y +  + IK+L  E VG++    +  D  G+S+G   V +        A++ 
Sbjct: 1  RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60

Query: 84 YNNVQLDGKPMKIE 97
           N   L+G+P+ I+
Sbjct: 61 MNKYDLNGRPLNIK 74

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 36.0 bits (84), Expect = 0.001
 Identities = 20/67 (29%), Positives = 36/67 (53%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          ++I NLD  + N+ + + FS  G++    +  D +G SKG   V +     AV A+++ N
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 86 NVQLDGK 92
           + L+ K
Sbjct: 65 GMLLNDK 71

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

>gnl|CDD|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 = 36.3 bits (84), Expect = 0.001
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAV 81
          KL++  L    + +D++ LF   G ++  +I     G SKG A V +S  A+A AA+
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI 59

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 19/72 (26%), Positives = 38/72 (52%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          ++++  +D+  +  D+++ FS+ G +K   I  DR+G SKG   V +  + DA   ++  
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63

Query: 85 NNVQLDGKPMKI 96
          N +    K + I
Sbjct: 64 NRLCFRDKKLNI 75

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|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5)

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 37/160 (23%), Positives = 53/160 (33%), Gaps = 19/160 (11%)

Query: 16  RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKG--TAEVVYSR 73
           R + +E  TK  +  L  G+S E  K + +   D ++  +       + G  T   + + 
Sbjct: 382 RLTYVEDLTKATMKKLTQGMS-EHSKAMSTAKTDEEKEELKTKEQLTTTGLRTCNNILAM 440

Query: 74  RADAVAAV---KRYNNVQLDGKPMKIEIVGTNIATRTAAPA--ANVNFGNSNGVPRGGQ- 127
             D   +    K    + L     K   +G  I      PA     N       P   Q 
Sbjct: 441 TKDLFHSPPIFKHDLAIVLSWIVPKNNKLGKPITFGGKRPANGKGNNVPAKKSRPSNDQK 500

Query: 128 ----------GRGGAFRRLRGGGGGGGRGFGRGRGRGRER 157
                      + G     RG   G GRG G GRGRG  R
Sbjct: 501 QYVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNR 540

This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors. Length = 543

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          +L++ NL   ++ E+ KELFS+ G++    ++ +     KG   +    R +A  A    
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAEL 57

Query: 85 NNVQLDGKPMKI 96
          + +   G+ +++
Sbjct: 58 DGIMRKGRQLRV 69

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVK 82
          T L I+ L   +++E+ + LF  VG +K   I  D R+G S G   V Y    DA  A++
Sbjct: 1  TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 83 RYNNVQLDGKPMKI 96
            N +QL  K +K+
Sbjct: 61 TLNGLQLQNKRIKV 74

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

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          LY+ NL    + E I++ F+ +   K  ++  +R  + +  A V +S R DAV A+   N
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSI---KPGAV--ERVKKIRDYAFVHFSNREDAVDAMNALN 65

Query: 86 NVQLDGKPMKIEI 98
             +DG P+++ +
Sbjct: 66 GKVIDGSPIEVTL 78

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

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          ++ T L ++ L   ++ E++K LF  +G+++   +  D+ +G+S G   V Y    DA  
Sbjct: 2  DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 80 AVKRYNNVQLDGKPMKI 96
          A+   N ++L  K +K+
Sbjct: 62 AINTLNGLRLQTKTIKV 78

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 18/61 (29%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          LYIS L   ++ +D++++FS  G +    +  D+ +G S+G A + + +R++A  A+  +
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 85 N 85
          N
Sbjct: 63 N 63

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

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 9/82 (10%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLK--------RYSIHYDR-SGRSKGTAEVVYSRRAD 76
          +Y+  L+  V+ E++ + F   G +K          +I+ D+ +G+ KG A V Y     
Sbjct: 3  IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62

Query: 77 AVAAVKRYNNVQLDGKPMKIEI 98
          A AAV+ ++     G  +K+ +
Sbjct: 63 AKAAVEWFDGKDFQGSKLKVSL 84

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 18/30 (60%), Positives = 18/30 (60%)

Query: 131 GAFRRLRGGGGGGGRGFGRGRGRGRERNEK 160
           G   R  G  G GGRG GRGRGRG E  EK
Sbjct: 6   GGEGRGFGRRGRGGRGRGRGRGRGGEGEEK 35

Length = 257

>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 = 35.4 bits (81), Expect = 0.002
 Identities = 20/64 (31%), Positives = 32/64 (50%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL+I  +    +  DI+ +FS  G ++   I     G S+G A V ++ RA A  A+K  
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 62

Query: 85 NNVQ 88
          +  Q
Sbjct: 63 HQAQ 66

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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVV--YSRRADAVAAVKR 83
          L I NLD  VS+E ++ +F   GD+K       R    K     V  +  R DA  A++ 
Sbjct: 4  LVIFNLDPTVSSETLRSIFQVYGDVKEL-----RETPCKREQRFVEFFDVR-DAAKALRA 57

Query: 84 YNNVQLDGKPMKIE 97
           N  ++ GKP+ IE
Sbjct: 58 MNGKEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          LY+ +LD  V+   + +LF   G +    +  D  + RS G   V +   ADA  A++  
Sbjct: 3  LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 85 NNVQLDGKPMKI 96
          N  +L GKP++I
Sbjct: 63 NFKRLGGKPIRI 74

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 22/45 (48%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 117 GNSNGVPRGGQGRGGAFRRLRGGGGGGGRGFGRGRGRGRERNEKI 161
           G   G  RGG GRGG     RG G GGG G GRG G G    + I
Sbjct: 15  GGGGGGGRGGGGRGGGRGGGRGRGRGGGGG-GRGGGGGGGPGKVI 58

Length = 293

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 17/74 (22%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T LY+  L   V+ +D+++ F + G+++  ++        +  A V ++ R  A  A +R
Sbjct: 2  TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV-----PRQQCAFVTFTTREAAEKAAER 56

Query: 84 -YNNVQLDGKPMKI 96
           +N + ++G+ +K+
Sbjct: 57 LFNKLIINGRRLKL 70

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          L + NL   VSNE ++E FS  G ++R  +  D  GR  G   V ++ +  A  A+ R
Sbjct: 2  LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR 59

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.9
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.82
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.77
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.75
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.74
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.74
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.73
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.73
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.73
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.73
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.7
KOG0122	270	consensus Translation initiation factor 3, subunit	99.7
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.69
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.67
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.67
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.67
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.65
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.64
PLN03120	260	nucleic acid binding protein; Provisional	99.64
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.63
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.61
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.6
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.6
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.6
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.59
PLN03213	759	repressor of silencing 3; Provisional	99.59
smart00362	72	RRM_2 RNA recognition motif.	99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
PLN03121	243	nucleic acid binding protein; Provisional	99.58
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.56
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.55
smart00360	71	RRM RNA recognition motif.	99.55
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.55
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.54
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.53
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.53
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.53
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.53
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.51
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.51
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.51
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.51
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.5
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.49
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.48
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.46
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.46
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.46
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.42
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.4
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.39
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.38
smart00361	70	RRM_1 RNA recognition motif.	99.37
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.35
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.34
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.32
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.32
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.29
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.27
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.24
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.21
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.18
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.17
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.12
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.12
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.12
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.11
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.11
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.09
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.07
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.05
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.05
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.02
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.01
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.99
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.98
PF13865	74	FoP_duplication: C-terminal duplication domain of	98.98
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.97
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.91
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.88
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.78
KOG0151	877	consensus Predicted splicing regulator, contains R	98.75
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.72
KOG0226	290	consensus RNA-binding proteins [General function p	98.7
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.66
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.64
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.61
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.55
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.54
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.53
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.35
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.34
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.24
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.24
KOG4210	285	consensus Nuclear localization sequence binding pr	98.18
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.18
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.16
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.09
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.08
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.05
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.05
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.93
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.93
KOG2314	698	consensus Translation initiation factor 3, subunit	97.92
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.89
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.87
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.79
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.78
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.6
KOG3152	278	consensus TBP-binding protein, activator of basal	97.6
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.6
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.55
PF13865	74	FoP_duplication: C-terminal duplication domain of	97.51
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.5
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.48
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.47
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.45
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.45
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.44
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.38
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.35
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.34
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.28
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.14
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.98
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.89
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.53
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.53
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.48
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.45
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.9
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.78
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.73
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.59
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.2
KOG2135	526	consensus Proteins containing the RNA recognition	95.12
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.89
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.62
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.48
KOG4660	549	consensus Protein Mei2, essential for commitment t	94.23
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.96
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.77
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.39
KOG4210	285	consensus Nuclear localization sequence binding pr	92.81
KOG2318	650	consensus Uncharacterized conserved protein [Funct	91.52
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	89.88
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	88.78
KOG4483	528	consensus Uncharacterized conserved protein [Funct	86.93
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	81.18

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

Probab=99.90  E-value=1.6e-22  Score=148.13  Aligned_cols=91  Identities=24%  Similarity=0.452  Sum_probs=84.0

Q ss_pred             CCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           12 QQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        12 ~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      ..+...+....+++|||+|||+.++|++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.
T Consensus        23 ~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~  102 (144)
T PLN03134         23 VTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN  102 (144)
T ss_pred             cccccccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            345556667889999999999999999999999999999999999998 8999999999999999999999999999999


Q ss_pred             CceEEEEEeeCC
Q 030010           91 GKPMKIEIVGTN  102 (184)
Q Consensus        91 g~~i~V~~~~~~  102 (184)
                      ++.|+|+++..+
T Consensus       103 Gr~l~V~~a~~~  114 (144)
T PLN03134        103 GRHIRVNPANDR  114 (144)
T ss_pred             CEEEEEEeCCcC
Confidence            999999998754

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.82  E-value=7.5e-19  Score=137.47  Aligned_cols=156  Identities=45%  Similarity=0.687  Sum_probs=105.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .....++|+|.|||+.|+++||+++|.+|+.++.+.+.+++.+.+.|+|-|.|...++|.+||+.|++..++|+.|+|.+
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            44445899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCCCCCCCCC-CCCCCCC-CCCCC-CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCChhhHhHHHHHH
Q 030010           99 VGTNIATRTAAP-AANVNFG-NSNGV-PRGGQGRGGAFRRL--RGGGGGGGRGFGRGRGRGRERNEKISAEDLDADLDKY  173 (184)
Q Consensus        99 ~~~~~~~~~~~~-~~~~~~~-~~~~~-~~~~~~~gg~~g~g--~ggg~~g~~g~~~g~~~g~~r~~~~~~~~lD~el~~y  173 (184)
                      ..+........- .....+. +..+. .+...+++. .+..  +++....++-...++...+....++++||||+|||+|
T Consensus       159 i~~~~~~~r~~~~~~~~~r~~~~~r~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~R~~k~~~tae~lDaeld~Y  237 (243)
T KOG0533|consen  159 ISSPSQSKRLPVGATKPLRAPNSNRTPARVSRGDKA-SGASKRRRGAGRPGGKFKGGKRGKREAKPEKTAEELDAELDAY  237 (243)
T ss_pred             ecCccccccccccccccccccccccccccccCCCCc-cCcccccCCCccccccccCCCCCCcCCcCcccHHHHHHHHHHH
Confidence            887554432110 0000000 00010 000001100 0001  1111100111122223344577799999999999999


Q ss_pred             hh
Q 030010          174 YS  175 (184)
Q Consensus       174 ~~  175 (184)
                      |+
T Consensus       238 ~~  239 (243)
T KOG0533|consen  238 MA  239 (243)
T ss_pred             Hh
Confidence            99

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.82  E-value=5e-19  Score=146.50  Aligned_cols=84  Identities=25%  Similarity=0.522  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMKIE   97 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V~   97 (184)
                      ...++|||+|||+.++|++|+++|++||.|+.|+|+.++ ++++++||||+|.+.++|++||+.||+..|.+  ++|+|.
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~  270 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR  270 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            346789999999999999999999999999999999998 89999999999999999999999999998876  688888


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      +++....
T Consensus       271 ~a~~~~~  277 (346)
T TIGR01659       271 LAEEHGK  277 (346)
T ss_pred             ECCcccc
Confidence            8876543

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.77  E-value=4.9e-18  Score=140.79  Aligned_cols=84  Identities=18%  Similarity=0.266  Sum_probs=78.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...+.+|||+|||+.+++++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|.+||..||+..|.|+.|+|.+
T Consensus       266 ~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~  345 (352)
T TIGR01661       266 DGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF  345 (352)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3445689999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +..+.
T Consensus       346 ~~~~~  350 (352)
T TIGR01661       346 KTNKA  350 (352)
T ss_pred             ccCCC
Confidence            88654

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.75  E-value=1.2e-17  Score=138.21  Aligned_cols=84  Identities=25%  Similarity=0.408  Sum_probs=79.0

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ......++|||+|||++++|++|+++|++||+|+.|+|+.++ ++++++||||+|.++++|++||+.||+..|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            455578999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEeeC
Q 030010           97 EIVGT  101 (184)
Q Consensus        97 ~~~~~  101 (184)
                      .++++
T Consensus       182 ~~a~p  186 (346)
T TIGR01659       182 SYARP  186 (346)
T ss_pred             ecccc
Confidence            98765

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.74  E-value=1.7e-17  Score=137.63  Aligned_cols=83  Identities=29%  Similarity=0.492  Sum_probs=78.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ++.++|||+|||..++|++|+++|++||+|..|+|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|+++
T Consensus         1 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a   80 (352)
T TIGR01661         1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA   80 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee
Confidence            357899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             eCCC
Q 030010          100 GTNI  103 (184)
Q Consensus       100 ~~~~  103 (184)
                      ++..
T Consensus        81 ~~~~   84 (352)
T TIGR01661        81 RPSS   84 (352)
T ss_pred             cccc
Confidence            7544

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.74  E-value=2.2e-17  Score=105.56  Aligned_cols=70  Identities=30%  Similarity=0.599  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      |||+|||..+++++|+++|++||.|..+.+..+.++..+++|||+|.+.++|++|++.|++..+.+++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999999999887888999999999999999999999999999999885

(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 ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.73  E-value=1.4e-16  Score=117.22  Aligned_cols=81  Identities=22%  Similarity=0.353  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ....++|||+||+..+++.+|+.+|..||+|..|.|-..    +.|||||||+++.+|+.|+..|++..|.|..|+|+++
T Consensus         7 ~~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    7 RNGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             cCCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            455899999999999999999999999999999988764    4789999999999999999999999999999999999


Q ss_pred             eCCCC
Q 030010          100 GTNIA  104 (184)
Q Consensus       100 ~~~~~  104 (184)
                      +....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            86544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.73  E-value=3.5e-17  Score=121.46  Aligned_cols=79  Identities=19%  Similarity=0.346  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ...++|||+|||..+.|.+|+++|.+||.|..|.|...+  .+..||||+|+++.+|+.||..-++..++++.|+|++.+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            457899999999999999999999999999999886433  235699999999999999999999999999999999986


Q ss_pred             C
Q 030010          101 T  101 (184)
Q Consensus       101 ~  101 (184)
                      .
T Consensus        82 g   82 (241)
T KOG0105|consen   82 G   82 (241)
T ss_pred             C
Confidence            4

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.73  E-value=1.3e-17  Score=116.79  Aligned_cols=83  Identities=31%  Similarity=0.528  Sum_probs=77.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....+++|||+||++.++|++|.+||+++|+|..|-+-.|+ +..+.|||||+|.+.++|+.|++.+++..++.++|+|.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            44568999999999999999999999999999999999999 77899999999999999999999999999999999999


Q ss_pred             EeeC
Q 030010           98 IVGT  101 (184)
Q Consensus        98 ~~~~  101 (184)
                      |...
T Consensus       112 ~D~G  115 (153)
T KOG0121|consen  112 WDAG  115 (153)
T ss_pred             cccc
Confidence            8653

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

Probab=99.73  E-value=1.5e-16  Score=138.62  Aligned_cols=78  Identities=27%  Similarity=0.375  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhC--CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEV--GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~--G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....++|||+||++++++++|+++|++|  |.|++|+++       ++||||+|.+.++|++||+.||+.+|.|+.|+|+
T Consensus       230 ~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             cccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4456899999999999999999999999  999999876       4599999999999999999999999999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ++++...
T Consensus       303 ~Akp~~~  309 (578)
T TIGR01648       303 LAKPVDK  309 (578)
T ss_pred             EccCCCc
Confidence            9987544

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.

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.70  E-value=6e-17  Score=114.50  Aligned_cols=88  Identities=24%  Similarity=0.394  Sum_probs=82.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      |.-...++.|||.+++..++|++|.+.|..||+|++|++..|+ ++..+|||+|+|++.++|++||..+|+..|.++.|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            4556678999999999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q 030010           96 IEIVGTNIA  104 (184)
Q Consensus        96 V~~~~~~~~  104 (184)
                      |.|+..+.+
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999987554

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.70  E-value=1.8e-16  Score=122.09  Aligned_cols=84  Identities=26%  Similarity=0.424  Sum_probs=80.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ..+..++|.|.||+.+++|.+|.+||..||.|.+|.|.+|+ +|.++|||||.|.+.++|.+||..|||+-++.-.|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            45578899999999999999999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      |+++.
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99874

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.69  E-value=2.8e-16  Score=118.41  Aligned_cols=90  Identities=26%  Similarity=0.427  Sum_probs=84.8

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ..|+..+.-++|.|-||.+-++.++|..+|++||.|-.|.|..|+ +..++|||||-|.+..+|+.|+++|++..|+|+.
T Consensus         5 ~~PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRe   84 (256)
T KOG4207|consen    5 RPPPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRE   84 (256)
T ss_pred             CCCCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccce
Confidence            447888888999999999999999999999999999999999999 9999999999999999999999999999999999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      |+|++++-...
T Consensus        85 lrVq~arygr~   95 (256)
T KOG4207|consen   85 LRVQMARYGRP   95 (256)
T ss_pred             eeehhhhcCCC
Confidence            99999986544

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=2.8e-15  Score=118.39  Aligned_cols=90  Identities=23%  Similarity=0.439  Sum_probs=83.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ...++-++|||.-|++.++|..|+..|+.||+|+.|.|+.++ +++++|||||+|+++.++..|.+..++..|+++.|.|
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~V  175 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILV  175 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEE
Confidence            344778999999999999999999999999999999999998 9999999999999999999999999999999999999


Q ss_pred             EEeeCCCCCCC
Q 030010           97 EIVGTNIATRT  107 (184)
Q Consensus        97 ~~~~~~~~~~~  107 (184)
                      .+-........
T Consensus       176 DvERgRTvkgW  186 (335)
T KOG0113|consen  176 DVERGRTVKGW  186 (335)
T ss_pred             Eeccccccccc
Confidence            99887666544

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.67  E-value=4e-16  Score=124.58  Aligned_cols=91  Identities=21%  Similarity=0.391  Sum_probs=81.6

Q ss_pred             CCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           13 QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        13 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      .+...+..+..++|||+|||+...|-||+.+|.+||+|..|+|+.+..| +|||+||+|++.++|++|-++||+..+.|+
T Consensus        86 ~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGR  164 (376)
T KOG0125|consen   86 PSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGR  164 (376)
T ss_pred             CCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeece
Confidence            4455667777899999999999999999999999999999999988643 489999999999999999999999999999


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      +|.|..+.....
T Consensus       165 kIEVn~ATarV~  176 (376)
T KOG0125|consen  165 KIEVNNATARVH  176 (376)
T ss_pred             EEEEeccchhhc
Confidence            999998876543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.67  E-value=6.8e-16  Score=99.13  Aligned_cols=70  Identities=31%  Similarity=0.581  Sum_probs=64.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      |||+|||+++++++|.++|+.||.|..+.+..++.+.++++|||+|.+.++|++|++.+++..|.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999999988788999999999999999999999999999999874

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 ....

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=2e-15  Score=124.73  Aligned_cols=93  Identities=22%  Similarity=0.416  Sum_probs=83.8

Q ss_pred             CCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 030010           10 PVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQ   88 (184)
Q Consensus        10 ~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~   88 (184)
                      ||.+|..+.+ .-+|-|||+.||.++.|++|.-||++.|+|-.++|++|+ +|.++|||||+|.+.++|++||+.||+++
T Consensus        71 PpP~weg~~p-~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~E  149 (506)
T KOG0117|consen   71 PPPGWEGPPP-PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYE  149 (506)
T ss_pred             CCCcccCCCC-CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcc
Confidence            4444666555 669999999999999999999999999999999999998 99999999999999999999999999999


Q ss_pred             cC-CceEEEEEeeCCC
Q 030010           89 LD-GKPMKIEIVGTNI  103 (184)
Q Consensus        89 ~~-g~~i~V~~~~~~~  103 (184)
                      |. |+.|.|+++...-
T Consensus       150 ir~GK~igvc~Svan~  165 (506)
T KOG0117|consen  150 IRPGKLLGVCVSVANC  165 (506)
T ss_pred             ccCCCEeEEEEeeecc
Confidence            96 8999999887543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.64  E-value=1e-15  Score=117.32  Aligned_cols=82  Identities=24%  Similarity=0.418  Sum_probs=75.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      .+..-++|||++|+|++..++|+++|++||+|.+..|+.|+ +++++||+||+|.+.+.|.+|++. .+..|+|++..+.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            45567899999999999999999999999999999999999 999999999999999999999964 6688999999999


Q ss_pred             EeeC
Q 030010           98 IVGT  101 (184)
Q Consensus        98 ~~~~  101 (184)
                      ++.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            8865

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.64  E-value=2.1e-15  Score=118.74  Aligned_cols=78  Identities=19%  Similarity=0.257  Sum_probs=71.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      .++|||+|||+.++|++|+++|+.||.|..|.|+.++.  .++||||+|.++++|+.||. |++..|.|+.|+|.++..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            57999999999999999999999999999999988763  46899999999999999994 9999999999999998754


Q ss_pred             C
Q 030010          103 I  103 (184)
Q Consensus       103 ~  103 (184)
                      .
T Consensus        81 ~   81 (260)
T PLN03120         81 Q   81 (260)
T ss_pred             C
Confidence            3

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

Probab=99.63  E-value=2.6e-15  Score=131.32  Aligned_cols=83  Identities=18%  Similarity=0.318  Sum_probs=78.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ...++|||+|||.++++++|+++|+.||.|..|+|..++ +++++|||||+|.+.++|.+||+.||+.+|+|+.|+|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            346899999999999999999999999999999999998 7889999999999999999999999999999999999998


Q ss_pred             eCCC
Q 030010          100 GTNI  103 (184)
Q Consensus       100 ~~~~  103 (184)
                      .++.
T Consensus       282 i~pP  285 (612)
T TIGR01645       282 VTPP  285 (612)
T ss_pred             CCCc
Confidence            8644

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.

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

Probab=99.62  E-value=2.5e-15  Score=131.39  Aligned_cols=82  Identities=23%  Similarity=0.459  Sum_probs=77.0

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ......++|||+|||+.+++++|+++|.+||.|..|+|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus       102 ~a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV  181 (612)
T TIGR01645       102 QALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKV  181 (612)
T ss_pred             hhhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeee
Confidence            445567999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEe
Q 030010           97 EIV   99 (184)
Q Consensus        97 ~~~   99 (184)
                      ...
T Consensus       182 ~rp  184 (612)
T TIGR01645       182 GRP  184 (612)
T ss_pred             ccc
Confidence            854

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.

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

Probab=99.61  E-value=3.6e-15  Score=130.00  Aligned_cols=78  Identities=22%  Similarity=0.434  Sum_probs=71.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPMKIE   97 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i~V~   97 (184)
                      ....++|||+|||++++|++|+++|++||.|..|+|++|.++++++||||+|.+.++|++||+.||+.+|. ++.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            44579999999999999999999999999999999999999999999999999999999999999998885 5665554

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=99.60  E-value=5.3e-15  Score=129.98  Aligned_cols=78  Identities=29%  Similarity=0.445  Sum_probs=74.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .+|||+|||.++||++|+++|++||.|..|+|+++. +++++|||||+|.+.++|++||+.|++..|.|+.|+|.++..
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            379999999999999999999999999999999998 799999999999999999999999999999999999998753

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

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.60  E-value=1.5e-14  Score=119.54  Aligned_cols=82  Identities=21%  Similarity=0.474  Sum_probs=76.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHh-hCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFS-EVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~-~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ...+||+|||+++.|++|++||. +.|+|++|++..|.++++++||.|||+++|.+++|+++||.+++.|++|.|.....
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            35599999999999999999996 78999999999999999999999999999999999999999999999999987765


Q ss_pred             CCC
Q 030010          102 NIA  104 (184)
Q Consensus       102 ~~~  104 (184)
                      ...
T Consensus       124 ~q~  126 (608)
T KOG4212|consen  124 EQR  126 (608)
T ss_pred             hhh
Confidence            443

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

Probab=99.60  E-value=1.2e-14  Score=126.24  Aligned_cols=83  Identities=25%  Similarity=0.411  Sum_probs=77.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ....++|||+|||+.+++++|+++|++||.|..+.|+.+. ++.++|||||+|.+.++|+.||+.||+..|.++.|.|.+
T Consensus       292 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~  371 (509)
T TIGR01642       292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQR  371 (509)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456899999999999999999999999999999999987 899999999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +...
T Consensus       372 a~~~  375 (509)
T TIGR01642       372 ACVG  375 (509)
T ss_pred             CccC
Confidence            8653

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

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

Probab=99.59  E-value=1.2e-14  Score=124.64  Aligned_cols=81  Identities=27%  Similarity=0.589  Sum_probs=76.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+. ++++++||||+|.+.++|++|++.||+..|.|+.|+|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            37899999999999999999999999999999999998 77999999999999999999999999999999999999987


Q ss_pred             CC
Q 030010          101 TN  102 (184)
Q Consensus       101 ~~  102 (184)
                      ..
T Consensus       265 ~~  266 (457)
T TIGR01622       265 DS  266 (457)
T ss_pred             CC
Confidence            43

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.59  E-value=5.8e-15  Score=123.62  Aligned_cols=79  Identities=19%  Similarity=0.347  Sum_probs=72.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCH--HHHHHHHHHhCCCccCCceEEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR--ADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~--e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ....+|||+||++.+++++|+.+|+.||.|..|.|++. ++  +|||||+|.+.  .++.+||..||+..+.|+.|+|..
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            44689999999999999999999999999999999933 55  89999999987  789999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8874

>smart00362 RRM_2 RNA recognition motif

Probab=99.59  E-value=1.4e-14  Score=91.83  Aligned_cols=72  Identities=39%  Similarity=0.664  Sum_probs=66.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      +|||+|||..+++++|+++|.+||.|..+.+..++ +.++++|||+|.+.++|++|++.+++..+.++.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998776 6778999999999999999999999999999988863

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

Probab=99.59  E-value=1.1e-14  Score=128.11  Aligned_cols=84  Identities=32%  Similarity=0.539  Sum_probs=79.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ....++|||+||++.+++++|+++|++||.|..|+|+.+.++.++|||||+|.+.++|++||..||+..|.|++|.|.++
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            44578899999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             eCCC
Q 030010          100 GTNI  103 (184)
Q Consensus       100 ~~~~  103 (184)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            8643

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

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.58  E-value=2.3e-14  Score=111.31  Aligned_cols=77  Identities=19%  Similarity=0.229  Sum_probs=70.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .+++|||+||++.+||++|+++|+.||+|..|+|+.+.  ...+||||+|.++++++.|+ .|++..|.++.|.|..+..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            46899999999999999999999999999999999874  44579999999999999999 6999999999999988764

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.56  E-value=1e-14  Score=107.97  Aligned_cols=85  Identities=29%  Similarity=0.435  Sum_probs=79.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .+.+...+|||+||+..++++.|+++|-+.|+|..++|..++ +...+|||||+|.++|+|+-||+.||...|.|++|+|
T Consensus         4 ~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv   83 (203)
T KOG0131|consen    4 IERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRV   83 (203)
T ss_pred             cccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEE
Confidence            345678999999999999999999999999999999999999 8889999999999999999999999999999999999


Q ss_pred             EEeeCC
Q 030010           97 EIVGTN  102 (184)
Q Consensus        97 ~~~~~~  102 (184)
                      ..+...
T Consensus        84 ~kas~~   89 (203)
T KOG0131|consen   84 NKASAH   89 (203)
T ss_pred             Eecccc
Confidence            998843

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

Probab=99.55  E-value=3.9e-14  Score=121.46  Aligned_cols=80  Identities=25%  Similarity=0.403  Sum_probs=74.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||. |++..|.|++|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            347899999999999999999999999999999999998 88999999999999999999995 8999999999999876


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            53

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.

>smart00360 RRM RNA recognition motif

Probab=99.55  E-value=4.8e-14  Score=88.95  Aligned_cols=70  Identities=36%  Similarity=0.644  Sum_probs=65.5

Q ss_pred             EcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           28 ISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        28 V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      |+|||..+++++|+++|.+||.|..+.+..++ +++++++|||+|.+.++|..|++.+++..+.++.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            67999999999999999999999999999887 68899999999999999999999999999999998873

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

Probab=99.55  E-value=7.1e-14  Score=120.84  Aligned_cols=80  Identities=25%  Similarity=0.323  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++++|||+||++ .+++++|+++|++||.|.+|+|+.++    ++||||+|.+.++|+.||..||+..|.|++|+|.+
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            45789999999998 69999999999999999999998764    58999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      ++...
T Consensus       348 s~~~~  352 (481)
T TIGR01649       348 SKQQN  352 (481)
T ss_pred             ccccc
Confidence            87643

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).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.54  E-value=5.5e-14  Score=116.32  Aligned_cols=81  Identities=31%  Similarity=0.466  Sum_probs=74.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      .....-+.|||.||+.+|||+.|+++|++||.|++|+.++|       ||||.|.+.++|.+|++.+|+.+|+|..|.|.
T Consensus       254 d~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iEvt  326 (506)
T KOG0117|consen  254 DTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIEVT  326 (506)
T ss_pred             hhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEEEE
Confidence            35556789999999999999999999999999999998754       99999999999999999999999999999999


Q ss_pred             EeeCCCCC
Q 030010           98 IVGTNIAT  105 (184)
Q Consensus        98 ~~~~~~~~  105 (184)
                      ++++....
T Consensus       327 LAKP~~k~  334 (506)
T KOG0117|consen  327 LAKPVDKK  334 (506)
T ss_pred             ecCChhhh
Confidence            99986543

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.53  E-value=1.4e-13  Score=87.58  Aligned_cols=74  Identities=35%  Similarity=0.613  Sum_probs=68.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      +|+|+|||..+++++|+++|..+|.|..+.+..+....+.++|||+|.+.++|+.|++.+++..+.++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999887557789999999999999999999999999999998864

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).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=8.1e-14  Score=108.59  Aligned_cols=86  Identities=16%  Similarity=0.263  Sum_probs=80.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      |.....+++|||-||.+++.|..|+++|..||.|..|+|++|- +.+++||+||.+.+.++|..||..||+..+.++.|.
T Consensus       272 p~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQ  351 (360)
T KOG0145|consen  272 PGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQ  351 (360)
T ss_pred             CCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEE
Confidence            4555568999999999999999999999999999999999999 799999999999999999999999999999999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |.+...+
T Consensus       352 VsFKtnk  358 (360)
T KOG0145|consen  352 VSFKTNK  358 (360)
T ss_pred             EEEecCC
Confidence            9998654

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=6.2e-14  Score=94.95  Aligned_cols=83  Identities=25%  Similarity=0.421  Sum_probs=74.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      -+.+....|||.|||+.+|.+++.++|.+||.|..|+|-..+  ..+|.|||.|++..+|++|+..|++..+.++.+.|-
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            445668899999999999999999999999999999987655  237899999999999999999999999999999998


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      +..+.
T Consensus        91 yyq~~   95 (124)
T KOG0114|consen   91 YYQPE   95 (124)
T ss_pred             ecCHH
Confidence            87653

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=4.6e-14  Score=109.92  Aligned_cols=86  Identities=24%  Similarity=0.452  Sum_probs=80.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ..+..+.|.|--||.++|+++|+.+|...|+|+.|++++|+ +|++.||+||.|.++++|++||..||+..+..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            35567889999999999999999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ++++...
T Consensus       117 yARPSs~  123 (360)
T KOG0145|consen  117 YARPSSD  123 (360)
T ss_pred             eccCChh
Confidence            9998643

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.51  E-value=9.9e-15  Score=111.12  Aligned_cols=84  Identities=24%  Similarity=0.406  Sum_probs=79.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .+...+|||++|..+|+|..|...|-.||.|..|.|..|. ++++++|+||+|...|+|.+||..||..+|.|+.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            4557899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +++..
T Consensus        87 AkP~k   91 (298)
T KOG0111|consen   87 AKPEK   91 (298)
T ss_pred             cCCcc
Confidence            99854

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

Probab=99.51  E-value=1e-13  Score=108.91  Aligned_cols=79  Identities=33%  Similarity=0.656  Sum_probs=76.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .++|||+|||..+++++|.++|.+||.|..|.+..++ ++++++||||+|.+.++|..|++.+++..|.++.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            6999999999999999999999999999999999997 899999999999999999999999999999999999999764

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.51  E-value=4.2e-13  Score=112.76  Aligned_cols=85  Identities=16%  Similarity=0.345  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      +......|||.|||.++++.+|+++|.+||.|+...|..-. .++..+|+||+|.+.++++.||++ +-..|++++|.|+
T Consensus       284 ~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Ve  362 (419)
T KOG0116|consen  284 PRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVE  362 (419)
T ss_pred             eeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEE
Confidence            33445669999999999999999999999999988876544 445448999999999999999986 5788999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ..++...
T Consensus       363 ek~~~~~  369 (419)
T KOG0116|consen  363 EKRPGFR  369 (419)
T ss_pred             ecccccc
Confidence            9876443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.51  E-value=2.4e-15  Score=111.31  Aligned_cols=82  Identities=26%  Similarity=0.527  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...+.-|||+|||+..||.||-.+|++||+|..|.+++|+ ||+++||||+.|++-.+...|+..|||..|.|+.|+|..
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            3457889999999999999999999999999999999999 999999999999999999999999999999999999987


Q ss_pred             eeC
Q 030010           99 VGT  101 (184)
Q Consensus        99 ~~~  101 (184)
                      ...
T Consensus       112 v~~  114 (219)
T KOG0126|consen  112 VSN  114 (219)
T ss_pred             ccc
Confidence            554

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.50  E-value=1.4e-13  Score=107.66  Aligned_cols=81  Identities=20%  Similarity=0.371  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .....|+|||+||+..++|++|++.|+.||+|.+|+|..+     +||+||.|+++|+|..||..+|+.+|.|+.+++.|
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            4456899999999999999999999999999999999866     67999999999999999999999999999999999


Q ss_pred             eeCCCC
Q 030010           99 VGTNIA  104 (184)
Q Consensus        99 ~~~~~~  104 (184)
                      -+....
T Consensus       235 GKe~~~  240 (321)
T KOG0148|consen  235 GKEGDD  240 (321)
T ss_pred             cccCCC
Confidence            886544

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.49  E-value=8.4e-14  Score=117.57  Aligned_cols=81  Identities=22%  Similarity=0.528  Sum_probs=78.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      +.|||+|||++++|++|..+|+..|.|..++++.|+ +|+++||+|++|.+.++|+.|++.||+.++.|++|+|.++...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            899999999999999999999999999999999999 9999999999999999999999999999999999999998865


Q ss_pred             CC
Q 030010          103 IA  104 (184)
Q Consensus       103 ~~  104 (184)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            54

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

Probab=99.48  E-value=2.2e-13  Score=117.85  Aligned_cols=75  Identities=19%  Similarity=0.197  Sum_probs=68.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCceEEEEEe
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY--NNVQLDGKPMKIEIV   99 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l--~g~~~~g~~i~V~~~   99 (184)
                      ++++|||+|||+.++|++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.|  ++..|.|+.|.|.++
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-----k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-----KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-----CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            5789999999999999999999999999999998854     569999999999999999875  678999999999998


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      ..
T Consensus        76 ~~   77 (481)
T TIGR01649        76 TS   77 (481)
T ss_pred             CC
Confidence            54

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).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.46  E-value=2.6e-13  Score=106.20  Aligned_cols=84  Identities=20%  Similarity=0.380  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...-..|||+.|...++-++|++.|.+||+|..++|++|. ++++|||+||.|.+.++|+.||..|||..|..+.|+-.|
T Consensus        59 ~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNW  138 (321)
T KOG0148|consen   59 SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNW  138 (321)
T ss_pred             cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccc
Confidence            3336789999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +..+.
T Consensus       139 ATRKp  143 (321)
T KOG0148|consen  139 ATRKP  143 (321)
T ss_pred             cccCc
Confidence            87654

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=7.6e-14  Score=115.12  Aligned_cols=86  Identities=28%  Similarity=0.476  Sum_probs=78.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccCC--ceEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN-VQLDG--KPMKIE   97 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g-~~~~g--~~i~V~   97 (184)
                      ...++|||+-|+..+||.+++++|++||.|+.|.|.++..+.++||+||.|.+.|.|..||+.||+ .++.|  .+|.|.
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            347899999999999999999999999999999999999999999999999999999999999999 55655  699999


Q ss_pred             EeeCCCCCC
Q 030010           98 IVGTNIATR  106 (184)
Q Consensus        98 ~~~~~~~~~  106 (184)
                      |+.+..+..
T Consensus       202 FADtqkdk~  210 (510)
T KOG0144|consen  202 FADTQKDKD  210 (510)
T ss_pred             ecccCCCch
Confidence            998876543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=1.8e-13  Score=112.92  Aligned_cols=85  Identities=26%  Similarity=0.488  Sum_probs=76.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCC-CccCC--ceEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNN-VQLDG--KPMKI   96 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g-~~~~g--~~i~V   96 (184)
                      ....++||+-||.+++|.||+++|++||.|.+|.|++|+ ++.++|||||.|.+.++|.+||.+||+ +.|.|  ++|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            456789999999999999999999999999999999999 899999999999999999999999998 55655  78888


Q ss_pred             EEeeCCCCC
Q 030010           97 EIVGTNIAT  105 (184)
Q Consensus        97 ~~~~~~~~~  105 (184)
                      .++..+...
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            888765443

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=3.1e-13  Score=105.71  Aligned_cols=88  Identities=23%  Similarity=0.331  Sum_probs=82.6

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ......+|.|||-.||.+..+.+|-++|-.||.|.+.++..|+ ++.+|+|+||.|+++.+++.||..|||..|.-++|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            3455679999999999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q 030010           96 IEIVGTNIA  104 (184)
Q Consensus        96 V~~~~~~~~  104 (184)
                      |.+.+++..
T Consensus       359 VQLKRPkda  367 (371)
T KOG0146|consen  359 VQLKRPKDA  367 (371)
T ss_pred             hhhcCcccc
Confidence            999987654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=9.9e-13  Score=111.35  Aligned_cols=85  Identities=25%  Similarity=0.406  Sum_probs=78.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .+.++|.|.||||.|...+|+.+|+.||.|..|.|.....++-+|||||.|.+..+|..||+.||+..|.|++|-|.|+.
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            44899999999999999999999999999999999977777777999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 030010          101 TNIAT  105 (184)
Q Consensus       101 ~~~~~  105 (184)
                      ++...
T Consensus       195 ~Kd~y  199 (678)
T KOG0127|consen  195 DKDTY  199 (678)
T ss_pred             ccccc
Confidence            76543

>PF13893 RRM_5: RNA recognition motif

Probab=99.40  E-value=2e-12  Score=79.53  Aligned_cols=56  Identities=30%  Similarity=0.578  Sum_probs=50.5

Q ss_pred             HHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           40 IKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        40 L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      |.++|++||+|..|.+..++    +++|||+|.+.++|+.|++.||+..+.|++|+|+++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999987554    479999999999999999999999999999999985

(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 ....

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=1.6e-12  Score=110.13  Aligned_cols=88  Identities=31%  Similarity=0.514  Sum_probs=78.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHh-----CC-Ccc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY-----NN-VQL   89 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l-----~g-~~~   89 (184)
                      +...+.+.+|||.|||+.+||+.|.++|++||+|..+.|+.++ ++.++|+|||.|.+..+|+.||+.-     .+ ..|
T Consensus       286 ~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll  365 (678)
T KOG0127|consen  286 RENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLL  365 (678)
T ss_pred             cccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEE
Confidence            4555667999999999999999999999999999999999999 9999999999999999999999865     23 678


Q ss_pred             CCceEEEEEeeCCCC
Q 030010           90 DGKPMKIEIVGTNIA  104 (184)
Q Consensus        90 ~g~~i~V~~~~~~~~  104 (184)
                      .|+.|.|.++-+...
T Consensus       366 ~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  366 DGRLLKVTLAVTRKE  380 (678)
T ss_pred             eccEEeeeeccchHH
Confidence            899999999876543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.38  E-value=7.8e-13  Score=106.97  Aligned_cols=84  Identities=19%  Similarity=0.348  Sum_probs=78.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      -.+|...|||..|.+.++.++|+-+|+.||+|..|.|++++ ++.+..||||+|++.+++++|.-+|++..|+++.|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            34567899999999999999999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      ++..-
T Consensus       315 FSQSV  319 (479)
T KOG0415|consen  315 FSQSV  319 (479)
T ss_pred             hhhhh
Confidence            87653

>smart00361 RRM_1 RNA recognition motif

Probab=99.37  E-value=3.4e-12  Score=82.19  Aligned_cols=61  Identities=28%  Similarity=0.502  Sum_probs=54.4

Q ss_pred             HHHHHHHHh----hCCCeEEEE-EEeCC-C--CCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           37 NEDIKELFS----EVGDLKRYS-IHYDR-S--GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        37 e~~L~~~f~----~~G~i~~v~-i~~~~-~--~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      +++|+++|+    +||.|.+|. |+.++ +  +.++||+||+|.+.++|.+|++.||+..+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578888888    999999995 66666 5  8899999999999999999999999999999998763

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.35  E-value=1.2e-12  Score=103.30  Aligned_cols=72  Identities=22%  Similarity=0.389  Sum_probs=68.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      .+|||+|||..+++.+|+.+|++||+|.+|.|+       |.|+||..++...+..||..||+.+|+|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-------KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-------cccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            479999999999999999999999999999999       449999999999999999999999999999999998876

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=9.6e-13  Score=106.89  Aligned_cols=76  Identities=24%  Similarity=0.482  Sum_probs=73.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      -|+|||+.|.+++.|+.|+..|..||+|++|.+..|. ++++++||||||+-+|.|+.|++.||+..+.|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            4899999999999999999999999999999999999 999999999999999999999999999999999999974

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.32  E-value=2.5e-12  Score=108.95  Aligned_cols=81  Identities=26%  Similarity=0.594  Sum_probs=76.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCCC
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIA  104 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~~  104 (184)
                      |||+||++++++++|+.+|+.||.|..|.+..|. +|.++||+||+|.+.++|.+|++.||+.+|-|+.|+|........
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            9999999999999999999999999999999998 999999999999999999999999999999999999998877655


Q ss_pred             CC
Q 030010          105 TR  106 (184)
Q Consensus       105 ~~  106 (184)
                      ..
T Consensus       361 ~~  362 (549)
T KOG0147|consen  361 TK  362 (549)
T ss_pred             cc
Confidence            44

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.32  E-value=7.9e-12  Score=104.41  Aligned_cols=78  Identities=27%  Similarity=0.484  Sum_probs=73.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCCCC
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIAT  105 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~~~  105 (184)
                      |||.||++.++..+|.++|+.||+|.+|++..+..+ +++| ||+|+++++|++||+.+|+..+.+++|.|.+...+...
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            999999999999999999999999999999999987 8999 99999999999999999999999999999887765543

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

Probab=99.29  E-value=1.9e-11  Score=106.22  Aligned_cols=77  Identities=16%  Similarity=0.275  Sum_probs=62.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhC------------CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEV------------GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~------------G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      .......+|||+|||+.+++++|+++|.++            +.|..+.+.     +.++||||+|.+.++|+.|| .|+
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-----~~kg~afVeF~~~e~A~~Al-~l~  243 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-----KEKNFAFLEFRTVEEATFAM-ALD  243 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-----CCCCEEEEEeCCHHHHhhhh-cCC
Confidence            334457899999999999999999999975            234444433     34789999999999999999 599


Q ss_pred             CCccCCceEEEEEee
Q 030010           86 NVQLDGKPMKIEIVG  100 (184)
Q Consensus        86 g~~~~g~~i~V~~~~  100 (184)
                      +..|.|..|+|....
T Consensus       244 g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       244 SIIYSNVFLKIRRPH  258 (509)
T ss_pred             CeEeeCceeEecCcc
Confidence            999999999987544

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

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.27  E-value=1.5e-11  Score=91.26  Aligned_cols=91  Identities=23%  Similarity=0.331  Sum_probs=81.9

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ........+..|||+||.++++|..|.++|+.||.|.. -+|+++. ++.+++|+||.|.+.+.+.+||..+|+..+..+
T Consensus        88 ~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr  167 (203)
T KOG0131|consen   88 AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNR  167 (203)
T ss_pred             cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCC
Confidence            55667778899999999999999999999999998854 5788888 799999999999999999999999999999999


Q ss_pred             eEEEEEeeCCCCC
Q 030010           93 PMKIEIVGTNIAT  105 (184)
Q Consensus        93 ~i~V~~~~~~~~~  105 (184)
                      +|+|+++..+...
T Consensus       168 ~itv~ya~k~~~k  180 (203)
T KOG0131|consen  168 PITVSYAFKKDTK  180 (203)
T ss_pred             ceEEEEEEecCCC
Confidence            9999999875543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.24  E-value=1.2e-11  Score=97.73  Aligned_cols=80  Identities=26%  Similarity=0.448  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ...+++|+|+||.+.++-++|+..|.+||+|.+++|+       ++|+||.|.-.++|..||+.|++.+|+|++++|.++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv-------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV-------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee-------cceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            4568999999999999999999999999999999999       459999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 030010          100 GTNIATR  106 (184)
Q Consensus       100 ~~~~~~~  106 (184)
                      .......
T Consensus       148 tsrlrta  154 (346)
T KOG0109|consen  148 TSRLRTA  154 (346)
T ss_pred             ccccccC
Confidence            8765443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.21  E-value=7.2e-11  Score=90.44  Aligned_cols=85  Identities=27%  Similarity=0.489  Sum_probs=74.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHH----HHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKE----LFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~----~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ...++..+|||.||+..+..++|+.    +|++||.|..|..  .++.+.+|-|||.|.+.+.|..|+..|+|..|.|++
T Consensus         4 ~~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a--~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~   81 (221)
T KOG4206|consen    4 MSVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISA--FKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKP   81 (221)
T ss_pred             cccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEe--cCCCCccCceEEEecChhHHHHHHHHhcCCcccCch
Confidence            4556677999999999999988877    9999999977654  456788999999999999999999999999999999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      ++|.+++.+..
T Consensus        82 mriqyA~s~sd   92 (221)
T KOG4206|consen   82 MRIQYAKSDSD   92 (221)
T ss_pred             hheecccCccc
Confidence            99999987654

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.18  E-value=6.7e-11  Score=100.99  Aligned_cols=82  Identities=22%  Similarity=0.348  Sum_probs=76.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      +..|||.+|...+...+|+.||++||+|.-.+|+.+. +.-.++|+||++.+.++|.+||+.||..+|.|+.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            5789999999999999999999999999999999887 666788999999999999999999999999999999999887


Q ss_pred             CCC
Q 030010          102 NIA  104 (184)
Q Consensus       102 ~~~  104 (184)
                      .+.
T Consensus       485 Ep~  487 (940)
T KOG4661|consen  485 EPG  487 (940)
T ss_pred             Ccc
Confidence            654

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.17  E-value=1.5e-10  Score=87.50  Aligned_cols=86  Identities=21%  Similarity=0.348  Sum_probs=78.6

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhC-CCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEV-GDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~-G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+.......+||..+|..+.+.+|..+|.++ |.|..+.+.+++ ||.+++||||+|++++.|+-|.+.||+..|.++-|
T Consensus        43 ~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL  122 (214)
T KOG4208|consen   43 KPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLL  122 (214)
T ss_pred             CCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhee
Confidence            4566677889999999999999999999988 788888887888 99999999999999999999999999999999999


Q ss_pred             EEEEeeCC
Q 030010           95 KIEIVGTN  102 (184)
Q Consensus        95 ~V~~~~~~  102 (184)
                      .|.+..+.
T Consensus       123 ~c~vmppe  130 (214)
T KOG4208|consen  123 ECHVMPPE  130 (214)
T ss_pred             eeEEeCch
Confidence            99998765

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=1.6e-10  Score=90.60  Aligned_cols=84  Identities=25%  Similarity=0.456  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccCC--ceEEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN-VQLDG--KPMKIEI   98 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g-~~~~g--~~i~V~~   98 (184)
                      ..++|||+-|...-.|+|++.+|..||.|.+|.+.+...+.+|||+||.|.+..+|+.||..||+ .++-|  ..|.|.+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            56899999999999999999999999999999999999999999999999999999999999999 45555  6899999


Q ss_pred             eeCCCCC
Q 030010           99 VGTNIAT  105 (184)
Q Consensus        99 ~~~~~~~  105 (184)
                      +.+..+.
T Consensus        98 ADTdkER  104 (371)
T KOG0146|consen   98 ADTDKER  104 (371)
T ss_pred             ccchHHH
Confidence            8876543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=2.3e-10  Score=92.46  Aligned_cols=82  Identities=24%  Similarity=0.329  Sum_probs=72.3

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC-CCccCCce
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN-NVQLDGKP   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~-g~~~~g~~   93 (184)
                      --|+.+...++|||++|-..++|.+|+++|.+||+|+.|.+...     +++|||+|.+.+.|+.|.+++- ...|+|.+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            34677788899999999989999999999999999999988754     4599999999999999887554 48889999


Q ss_pred             EEEEEeeC
Q 030010           94 MKIEIVGT  101 (184)
Q Consensus        94 i~V~~~~~  101 (184)
                      |.|.|.++
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999887

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.12  E-value=2.1e-10  Score=100.67  Aligned_cols=79  Identities=24%  Similarity=0.403  Sum_probs=72.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      +++|||+.|+..++|.+|..+|+.||+|.+|.++..     ++||||.+....+|.+|+.+|.+..+..+.|+|.|+...
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            689999999999999999999999999999988754     679999999999999999999999999999999999876


Q ss_pred             CCCC
Q 030010          103 IATR  106 (184)
Q Consensus       103 ~~~~  106 (184)
                      ....
T Consensus       496 G~ks  499 (894)
T KOG0132|consen  496 GPKS  499 (894)
T ss_pred             Ccch
Confidence            5443

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.11  E-value=2.4e-10  Score=94.96  Aligned_cols=79  Identities=27%  Similarity=0.431  Sum_probs=70.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .....+.|+|+|.|||+++||+.|++-|.+||.|.++.|+  ..+++++  .|.|.++++|+.|+..|++..+.|+.|+|
T Consensus       530 ~gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim--e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V  605 (608)
T KOG4212|consen  530 VGAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM--ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKV  605 (608)
T ss_pred             ccccccccEEEEecCCccccHHHHHHHHHhccceehhhhh--ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeee
Confidence            4566778999999999999999999999999999999884  3456665  89999999999999999999999999999


Q ss_pred             EEe
Q 030010           97 EIV   99 (184)
Q Consensus        97 ~~~   99 (184)
                      .+.
T Consensus       606 ~y~  608 (608)
T KOG4212|consen  606 TYF  608 (608)
T ss_pred             eeC
Confidence            873

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.11  E-value=2.5e-10  Score=92.93  Aligned_cols=102  Identities=16%  Similarity=0.285  Sum_probs=88.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHH
Q 030010            5 QVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR   83 (184)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~   83 (184)
                      +..+++.........+.....|||++||..+++++|++.|.+||.|..+.++.|. +.++++|+||+|.+++.+.+++. 
T Consensus        79 ~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-  157 (311)
T KOG4205|consen   79 PKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-  157 (311)
T ss_pred             ceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-
Confidence            3345555556666666678899999999999999999999999999999999998 88999999999999999999985 


Q ss_pred             hCCCccCCceEEEEEeeCCCCCCC
Q 030010           84 YNNVQLDGKPMKIEIVGTNIATRT  107 (184)
Q Consensus        84 l~g~~~~g~~i~V~~~~~~~~~~~  107 (184)
                      ..-+.|.++.+.|..+.++.....
T Consensus       158 ~~f~~~~gk~vevkrA~pk~~~~~  181 (311)
T KOG4205|consen  158 QKFHDFNGKKVEVKRAIPKEVMQS  181 (311)
T ss_pred             cceeeecCceeeEeeccchhhccc
Confidence            477999999999999998776554

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=3e-10  Score=92.57  Aligned_cols=81  Identities=19%  Similarity=0.320  Sum_probs=75.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      -.+|||..++++.+|+||+.+|+.||+|.+|.+-+.. ...++||+||||.+..+...||..||-..+.|+.|+|-.+-+
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            4799999999999999999999999999999999999 567999999999999999999999999999999999987665


Q ss_pred             CC
Q 030010          102 NI  103 (184)
Q Consensus       102 ~~  103 (184)
                      +.
T Consensus       290 PP  291 (544)
T KOG0124|consen  290 PP  291 (544)
T ss_pred             CC
Confidence            44

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.07  E-value=4.5e-10  Score=97.86  Aligned_cols=77  Identities=30%  Similarity=0.500  Sum_probs=70.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCC----cceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR----SKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~----~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ++|||.||++.++.++|..+|..+|.|..+.|...+...    +.||+||+|.++++|+.|++.|+++.|+|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            449999999999999999999999999999887766432    5599999999999999999999999999999999999


Q ss_pred             e
Q 030010          100 G  100 (184)
Q Consensus       100 ~  100 (184)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.05  E-value=6.9e-10  Score=92.83  Aligned_cols=75  Identities=28%  Similarity=0.340  Sum_probs=70.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNI  103 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~  103 (184)
                      .+|||+   +.|||.+|.++|+.+|+|..|++++|. . +.|||||.|.++++|++||..||...|.|++|+|.|+....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            468998   889999999999999999999999998 5 99999999999999999999999999999999999987533

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.05  E-value=8.6e-10  Score=89.15  Aligned_cols=82  Identities=24%  Similarity=0.425  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE--------EEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLK--------RYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~--------~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      ....+.|||+|||..+|.+++.++|++||-|.        .|+|+.+..|+.+|-+.|.|...+++..||+.|+...|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            44578899999999999999999999999775        4889999999999999999999999999999999999999


Q ss_pred             ceEEEEEeeC
Q 030010           92 KPMKIEIVGT  101 (184)
Q Consensus        92 ~~i~V~~~~~  101 (184)
                      +.|+|+.|+-
T Consensus       211 ~~~rVerAkf  220 (382)
T KOG1548|consen  211 KKLRVERAKF  220 (382)
T ss_pred             cEEEEehhhh
Confidence            9999998874

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.02  E-value=3.8e-10  Score=91.84  Aligned_cols=82  Identities=23%  Similarity=0.426  Sum_probs=74.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||++|+|.++++.|++.|.+||+|..|.++.++ ++++++|+||+|.+.+.+.++|. ...+.|.++.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            68999999999999999999999999999999999999 89999999999999999888885 35688999999988877


Q ss_pred             CCCC
Q 030010          101 TNIA  104 (184)
Q Consensus       101 ~~~~  104 (184)
                      +...
T Consensus        84 ~r~~   87 (311)
T KOG4205|consen   84 SRED   87 (311)
T ss_pred             Cccc
Confidence            6553

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.01  E-value=3.4e-10  Score=98.62  Aligned_cols=87  Identities=21%  Similarity=0.386  Sum_probs=77.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      +.....+.|+|.|||+..+-.+++.+|..||.|..|.|.... .+.++|||||+|-++.+|..|+..|....|.|+.|.+
T Consensus       608 ~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVL  687 (725)
T KOG0110|consen  608 SKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVL  687 (725)
T ss_pred             ccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhhe
Confidence            444447899999999999999999999999999999998664 5567999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      +|+.....
T Consensus       688 EwA~~d~~  695 (725)
T KOG0110|consen  688 EWAKSDNT  695 (725)
T ss_pred             ehhccchH
Confidence            99987543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.99  E-value=9.2e-09  Score=78.95  Aligned_cols=86  Identities=23%  Similarity=0.371  Sum_probs=70.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeC-C-CCCcceEEEEEecCHHHHHHHHHHhCCCccC---CceEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-R-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD---GKPMKI   96 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~-~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~---g~~i~V   96 (184)
                      .-.+|||.+||.++.-.+|..+|..|---+.+.|... + ...++-++||+|.+..+|++|+..|||..|+   ++.|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            3689999999999999999999998855555555443 3 2335679999999999999999999998887   689999


Q ss_pred             EEeeCCCCCCC
Q 030010           97 EIVGTNIATRT  107 (184)
Q Consensus        97 ~~~~~~~~~~~  107 (184)
                      ++++.......
T Consensus       113 ElAKSNtK~kr  123 (284)
T KOG1457|consen  113 ELAKSNTKRKR  123 (284)
T ss_pred             eehhcCccccc
Confidence            99987665444

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.98  E-value=2.4e-10  Score=87.22  Aligned_cols=83  Identities=24%  Similarity=0.261  Sum_probs=75.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..+...+|||.|+-..|+|+.|.++|-+.|+|.+|.|..++.++.+ ||||+|.++..+.-|++.+|+..+.+..|.|.+
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3345689999999999999999999999999999999988877777 999999999999999999999999999999987


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      ....
T Consensus        84 r~G~   87 (267)
T KOG4454|consen   84 RCGN   87 (267)
T ss_pred             ccCC
Confidence            6543

>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1

Probab=98.98  E-value=3.1e-09  Score=68.93  Aligned_cols=21  Identities=43%  Similarity=0.702  Sum_probs=18.8

Q ss_pred             CCCCCChhhHhHHHHHHhhHH
Q 030010          157 RNEKISAEDLDADLDKYYSEA  177 (184)
Q Consensus       157 r~~~~~~~~lD~el~~y~~~~  177 (184)
                      ..+++|+||||+|||+||+..
T Consensus        36 ~~~~kT~EeLDaELD~Ym~~~   56 (74)
T PF13865_consen   36 KKPPKTAEELDAELDAYMSKT   56 (74)
T ss_pred             CCCCCCHHHHHHHHHHHHHHH
Confidence            377999999999999999765

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.97  E-value=6.3e-09  Score=84.62  Aligned_cols=86  Identities=21%  Similarity=0.381  Sum_probs=77.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE--------EEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLK--------RYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~--------~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      ......+|||.+||..+++++|.++|.+++.|.        .|+|.+++ |+++|+-|.|.|.+...|+.||..+++..|
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            355578999999999999999999999999885        36788888 999999999999999999999999999999


Q ss_pred             CCceEEEEEeeCCCC
Q 030010           90 DGKPMKIEIVGTNIA  104 (184)
Q Consensus        90 ~g~~i~V~~~~~~~~  104 (184)
                      .+.+|+|.++.....
T Consensus       142 ~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  142 CGNTIKVSLAERRTG  156 (351)
T ss_pred             cCCCchhhhhhhccC
Confidence            999999999886554

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.91  E-value=4e-09  Score=82.84  Aligned_cols=85  Identities=22%  Similarity=0.383  Sum_probs=78.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ...+...+||+|+.+.++.++++.+|+.||.|..|.|..++ .+++++|+||+|.+.+.++.|+. |++..|.++.|.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            44567899999999999998899999999999999999999 77899999999999999999997 99999999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      +.....+
T Consensus       176 ~~r~~~p  182 (231)
T KOG4209|consen  176 LKRTNVP  182 (231)
T ss_pred             eeeeecC
Confidence            9887643

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.88  E-value=1.6e-09  Score=83.55  Aligned_cols=71  Identities=23%  Similarity=0.405  Sum_probs=65.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ..|||++||+.+.+.+|+.||..||+|..|.+.       .+|+||+|.+..+|..||..||+.+|.+..+.|+++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            479999999999999999999999999998876       56999999999999999999999999998888888763

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.78  E-value=3.3e-08  Score=83.35  Aligned_cols=81  Identities=20%  Similarity=0.357  Sum_probs=67.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .......|.+.+|||++|+++|.+||+.+ .|+.+.+.+ .+++..|-|||||.+.+++++|++ .+...+..+.|.|..
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR-RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFT   82 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec-cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEc
Confidence            34557788999999999999999999999 588754432 278999999999999999999996 488888999999987


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +...
T Consensus        83 ~~~~   86 (510)
T KOG4211|consen   83 AGGA   86 (510)
T ss_pred             cCCc
Confidence            7543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.75  E-value=3.2e-08  Score=86.62  Aligned_cols=83  Identities=25%  Similarity=0.332  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCC----CCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS----GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~----~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ...-.+.|||+||++.++|+.|...|..||+|..|+|+..++    .....|+||-|-+..+|++|++.|++..+....+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            345579999999999999999999999999999999987762    3467799999999999999999999999999999


Q ss_pred             EEEEeeC
Q 030010           95 KIEIVGT  101 (184)
Q Consensus        95 ~V~~~~~  101 (184)
                      ++-|.+.
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9999865

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.72  E-value=1.6e-08  Score=86.22  Aligned_cols=72  Identities=25%  Similarity=0.341  Sum_probs=64.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ..+..+|+|-|||..|++++|.++|+.||+|+.|..-..    ..+.+||+|.+..+|++|++.|+..+|.++.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            455789999999999999999999999999998665433    367899999999999999999999999999888

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.70  E-value=2.1e-08  Score=78.29  Aligned_cols=85  Identities=20%  Similarity=0.335  Sum_probs=76.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ..+...+||++.|..+++.+.|...|.+|-.....++++++ +++++||+||.|.+.+++..|+..|++..++.++|++.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            44557899999999999999999999999888888899998 99999999999999999999999999999999999887


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      .+..+.
T Consensus       266 kS~wke  271 (290)
T KOG0226|consen  266 KSEWKE  271 (290)
T ss_pred             hhhHHh
Confidence            665443

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

Probab=98.66  E-value=3.5e-07  Score=62.26  Aligned_cols=78  Identities=19%  Similarity=0.228  Sum_probs=66.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhh--CCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC----CceEEE
Q 030010           24 TKLYISNLDYGVSNEDIKELFSE--VGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD----GKPMKI   96 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~--~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~----g~~i~V   96 (184)
                      ++|.|.|||...|.++|.+++..  .|....+.+..|- +....|||||.|.+++.|.+-.+.+++..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999998864  3566777888787 7788999999999999999999999997775    467777


Q ss_pred             EEeeC
Q 030010           97 EIVGT  101 (184)
Q Consensus        97 ~~~~~  101 (184)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77764

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

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.64  E-value=1.6e-07  Score=77.81  Aligned_cols=79  Identities=25%  Similarity=0.377  Sum_probs=71.0

Q ss_pred             CCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .+.|.|.||... +|.+.|..+|+-||.|.+|+|..++    +.-|.|.|.+...|+.|++.|+++.|.|++|+|.+++-
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            688999999654 9999999999999999999999876    24799999999999999999999999999999999986


Q ss_pred             CCCC
Q 030010          102 NIAT  105 (184)
Q Consensus       102 ~~~~  105 (184)
                      ....
T Consensus       373 ~~vq  376 (492)
T KOG1190|consen  373 TNVQ  376 (492)
T ss_pred             cccc
Confidence            5543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.61  E-value=2.1e-07  Score=78.56  Aligned_cols=79  Identities=19%  Similarity=0.309  Sum_probs=67.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      .+...|.+.+||+.||+++|.+||+-.-.|.. |.++.+..+++.+-|||.|++.+.|++|+.. |...|..+.|.|..+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            56789999999999999999999998754444 5567777888999999999999999999975 888899999999765


Q ss_pred             e
Q 030010          100 G  100 (184)
Q Consensus       100 ~  100 (184)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.55  E-value=2.4e-07  Score=64.26  Aligned_cols=73  Identities=26%  Similarity=0.415  Sum_probs=45.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC-----CccCCceEEEE
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN-----VQLDGKPMKIE   97 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g-----~~~~g~~i~V~   97 (184)
                      ++.|+|.+++..++.++|+++|++|+.|..|.+....+     .|||-|.+.+.|+.|++.+.-     ..|.+..+.++
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~-----~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT-----EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S-----EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC-----EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            46899999999999999999999999999998875432     899999999999999986653     46677777777


Q ss_pred             Eee
Q 030010           98 IVG  100 (184)
Q Consensus        98 ~~~  100 (184)
                      +..
T Consensus        76 vLe   78 (105)
T PF08777_consen   76 VLE   78 (105)
T ss_dssp             ---
T ss_pred             ECC
Confidence            644

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

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.54  E-value=1.2e-07  Score=81.38  Aligned_cols=92  Identities=22%  Similarity=0.341  Sum_probs=83.1

Q ss_pred             CCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           12 QQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        12 ~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      ..+..+......+.|||++||..+++.++++++..||.++...++.+. ++-+++|||.+|.+......||..||+..+.
T Consensus       278 ~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lg  357 (500)
T KOG0120|consen  278 LLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLG  357 (500)
T ss_pred             CcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhc
Confidence            345556677778999999999999999999999999999999999888 7899999999999999999999999999999


Q ss_pred             CceEEEEEeeCCC
Q 030010           91 GKPMKIEIVGTNI  103 (184)
Q Consensus        91 g~~i~V~~~~~~~  103 (184)
                      +++|.|..+-...
T Consensus       358 d~~lvvq~A~~g~  370 (500)
T KOG0120|consen  358 DKKLVVQRAIVGA  370 (500)
T ss_pred             CceeEeehhhccc
Confidence            9999999876543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.53  E-value=1.6e-07  Score=76.38  Aligned_cols=79  Identities=18%  Similarity=0.270  Sum_probs=67.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCC--CeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVG--DLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G--~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...++||+||-|++|++||.+.+...|  .+..+++..++ +++++|||+|...+....++.++.|...+|.|+.-.|.-
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            346899999999999999988887665  56677888888 899999999999999999999999999999998666654


Q ss_pred             ee
Q 030010           99 VG  100 (184)
Q Consensus        99 ~~  100 (184)
                      ..
T Consensus       159 ~N  160 (498)
T KOG4849|consen  159 YN  160 (498)
T ss_pred             cc
Confidence            33

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

Probab=98.35  E-value=2.6e-06  Score=55.93  Aligned_cols=70  Identities=23%  Similarity=0.321  Sum_probs=47.8

Q ss_pred             CEEEEcCCCCCCCHHH----HHHHHhhCC-CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           24 TKLYISNLDYGVSNED----IKELFSEVG-DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~----L~~~f~~~G-~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      +.|||.|||....-..    |++++..+| .|..|  .       .+.|+|.|.+.+.|.+|.+.|++..+.|++|.|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~-------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S-------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e-------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            4689999999888655    667777776 55544  1       35899999999999999999999999999999998


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            7543

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

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.34  E-value=3.5e-07  Score=70.65  Aligned_cols=73  Identities=25%  Similarity=0.411  Sum_probs=64.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ..+....+.|.|.+|+..+.+.+|++.|..+|++....+.       .+++||+|.+.+++..||+.|++..+.++.|++
T Consensus        93 ~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   93 RPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             CCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            3456678999999999999999999999999998554442       459999999999999999999999999999999

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.24  E-value=1.5e-06  Score=66.96  Aligned_cols=69  Identities=22%  Similarity=0.326  Sum_probs=55.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      +....-.+|||-||..+|+|++|+.+|+.|--...++|. .+.|.+  +||++|++.+.|..|+..|+|..|
T Consensus       205 ~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~~g~~--vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  205 SGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR-ARGGMP--VAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             ccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cCCCcc--eEeecHHHHHHHHHHHHHhhccee
Confidence            344445789999999999999999999999765555543 344444  899999999999999998888655

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.24  E-value=1.7e-05  Score=65.31  Aligned_cols=84  Identities=23%  Similarity=0.322  Sum_probs=74.1

Q ss_pred             CCCCCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +....+++.+.|.+|... ++.+.|..+|-.||.|++|+++..+    .+.|.|++.+..+.++|+..||+..+-|.+|.
T Consensus       281 p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  281 PGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            466778899999999765 6778899999999999999999776    45799999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q 030010           96 IEIVGTNIA  104 (184)
Q Consensus        96 V~~~~~~~~  104 (184)
                      |.+++-...
T Consensus       357 v~~SkQ~~v  365 (494)
T KOG1456|consen  357 VCVSKQNFV  365 (494)
T ss_pred             Eeecccccc
Confidence            999886543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.18  E-value=2.1e-06  Score=69.66  Aligned_cols=85  Identities=24%  Similarity=0.438  Sum_probs=74.3

Q ss_pred             CCCCCCCEEE-EcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           18 SAIETGTKLY-ISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        18 ~~~~~~~~l~-V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ....+..++| |.+|+..+++++|+.+|..++.|..+++..++ ++.+++|+||+|.....+..++.. +...+.+.++.
T Consensus       179 ~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~  257 (285)
T KOG4210|consen  179 LSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLR  257 (285)
T ss_pred             cccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccc
Confidence            3444556666 99999999999999999999999999999888 899999999999999999999876 78899999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |....+..
T Consensus       258 ~~~~~~~~  265 (285)
T KOG4210|consen  258 LEEDEPRP  265 (285)
T ss_pred             cccCCCCc
Confidence            88876543

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.18  E-value=8.2e-07  Score=75.92  Aligned_cols=79  Identities=27%  Similarity=0.384  Sum_probs=72.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ..+||+--|+..++..+|.+||+.+|+|..|.|+.|+ +..++|.+||+|.+.+.+..|| .|.|..+.|.+|.|.....
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccHH
Confidence            4678888888889999999999999999999999999 8899999999999999999999 6899999999999987654


Q ss_pred             C
Q 030010          102 N  102 (184)
Q Consensus       102 ~  102 (184)
                      .
T Consensus       258 e  258 (549)
T KOG0147|consen  258 E  258 (549)
T ss_pred             H
Confidence            3

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.16  E-value=1.7e-05  Score=61.09  Aligned_cols=80  Identities=20%  Similarity=0.292  Sum_probs=68.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i~   95 (184)
                      .....+...+|+.|||.+++.+.|..+|.+|.-.+.|.++..+    .+.|||+|.+...+..|...+++..|- ...+.
T Consensus       140 ~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~  215 (221)
T KOG4206|consen  140 AQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQ  215 (221)
T ss_pred             ccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEE
Confidence            3446778999999999999999999999999888888888654    458999999999999999999997776 77888


Q ss_pred             EEEee
Q 030010           96 IEIVG  100 (184)
Q Consensus        96 V~~~~  100 (184)
                      |.+++
T Consensus       216 i~~a~  220 (221)
T KOG4206|consen  216 ITFAK  220 (221)
T ss_pred             ecccC
Confidence            87764

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.09  E-value=1.5e-05  Score=70.20  Aligned_cols=74  Identities=20%  Similarity=0.340  Sum_probs=66.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCe-EEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDL-KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i-~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .|-|.|+|+.++-+||-+||..|-.+ ..|.+.++..|+.+|-|-|.|++.++|.+|...|++..|..++|.|.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            78899999999999999999999554 456666666899999999999999999999999999999999998876

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.08  E-value=0.00015  Score=59.91  Aligned_cols=83  Identities=18%  Similarity=0.205  Sum_probs=66.5

Q ss_pred             CCCCCCCCEEEEcCC--CCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--c
Q 030010           17 ASAIETGTKLYISNL--DYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--K   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nL--p~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~   92 (184)
                      +....+.+.|.+.-|  -+.+|.+.|..+....|+|.+|.|... ++.   -|.|||++.+.|++|.+.||+..|.-  +
T Consensus       114 ~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCC  189 (494)
T KOG1456|consen  114 DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCC  189 (494)
T ss_pred             CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cce---eeEEeechhHHHHHHHhhcccccccccce
Confidence            344555666666655  445888999999999999999987643 433   69999999999999999999988874  6


Q ss_pred             eEEEEEeeCCC
Q 030010           93 PMKIEIVGTNI  103 (184)
Q Consensus        93 ~i~V~~~~~~~  103 (184)
                      +|+|+++++..
T Consensus       190 TLKIeyAkP~r  200 (494)
T KOG1456|consen  190 TLKIEYAKPTR  200 (494)
T ss_pred             eEEEEecCcce
Confidence            99999998864

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.05  E-value=0.00018  Score=54.22  Aligned_cols=76  Identities=24%  Similarity=0.371  Sum_probs=63.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC--CceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD--GKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~--g~~i   94 (184)
                      ++......+|.|++||...+|++|+++..+.|.|....+..|      +++.|+|...|+++-||.+|+...+.  |-..
T Consensus       109 ppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~  182 (241)
T KOG0105|consen  109 PPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETA  182 (241)
T ss_pred             CcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeeeeeehhhHHHHHHhhccccccCcCcEe
Confidence            566667889999999999999999999999999999888765      48999999999999999999886654  4444


Q ss_pred             EEEE
Q 030010           95 KIEI   98 (184)
Q Consensus        95 ~V~~   98 (184)
                      .|.+
T Consensus       183 yirv  186 (241)
T KOG0105|consen  183 YIRV  186 (241)
T ss_pred             eEEe
Confidence            4443

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.05  E-value=2.4e-05  Score=65.12  Aligned_cols=86  Identities=21%  Similarity=0.290  Sum_probs=67.5

Q ss_pred             CCCCCCC-CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-
Q 030010           14 AGRASAI-ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG-   91 (184)
Q Consensus        14 ~~~~~~~-~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g-   91 (184)
                      +...... .++.+|++.|+|..++|++|+.+|.+-|-..+......   +.+-++++.+.+.|+|..|+..++.+.+.. 
T Consensus       404 sKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---kd~kmal~q~~sveeA~~ali~~hnh~lgen  480 (492)
T KOG1190|consen  404 SKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---KDRKMALPQLESVEEAIQALIDLHNHYLGEN  480 (492)
T ss_pred             cccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---CCcceeecccCChhHhhhhccccccccCCCC
Confidence            3333334 66789999999999999999999998876544333222   234499999999999999999999999886 


Q ss_pred             ceEEEEEeeCC
Q 030010           92 KPMKIEIVGTN  102 (184)
Q Consensus        92 ~~i~V~~~~~~  102 (184)
                      ..|+|.+++..
T Consensus       481 ~hlRvSFSks~  491 (492)
T KOG1190|consen  481 HHLRVSFSKST  491 (492)
T ss_pred             ceEEEEeeccc
Confidence            48999998753

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.93  E-value=2.6e-05  Score=63.54  Aligned_cols=80  Identities=21%  Similarity=0.379  Sum_probs=61.7

Q ss_pred             CCEEEEcCCCCCCCHHH----H--HHHHhhCCCeEEEEEEeCC-CC-Ccce--EEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           23 GTKLYISNLDYGVSNED----I--KELFSEVGDLKRYSIHYDR-SG-RSKG--TAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~----L--~~~f~~~G~i~~v~i~~~~-~~-~~~g--~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ..-+||-+||+.+..++    |  .++|.+||.|.+|.|.... +. ...+  -.||+|.+.|+|.+||...++..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            45688989988765443    3  5789999999988776543 11 1112  259999999999999999999999999


Q ss_pred             eEEEEEeeCC
Q 030010           93 PMKIEIVGTN  102 (184)
Q Consensus        93 ~i~V~~~~~~  102 (184)
                      .|+..+-..+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999886554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.93  E-value=3e-05  Score=64.10  Aligned_cols=83  Identities=14%  Similarity=0.255  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCC-eEE--EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGD-LKR--YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~-i~~--v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ...+.-+|.+.+||++.+.++|..+|..|-. |..  |+++.+..|++.|-|||+|.+.|.|.+|..+.+++....+.|.
T Consensus       276 ~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiE  355 (508)
T KOG1365|consen  276 PTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIE  355 (508)
T ss_pred             CCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEE
Confidence            3344778999999999999999999998863 444  8888888999999999999999999999999888888889888


Q ss_pred             EEEeeC
Q 030010           96 IEIVGT  101 (184)
Q Consensus        96 V~~~~~  101 (184)
                      |.-+..
T Consensus       356 vfp~S~  361 (508)
T KOG1365|consen  356 VFPCSV  361 (508)
T ss_pred             EeeccH
Confidence            876554

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.92  E-value=4.3e-05  Score=65.93  Aligned_cols=80  Identities=21%  Similarity=0.276  Sum_probs=65.6

Q ss_pred             CCCEEEEcCCCCCCCH------HHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceE
Q 030010           22 TGTKLYISNLDYGVSN------EDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPM   94 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te------~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i   94 (184)
                      -...|+|-|+|..-..      .-|..+|+++|+|..+.+..+..+..+||.|++|.+..+|+.|++.|||+.|+ .++.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3578899999864221      23678899999999998888886679999999999999999999999998886 6788


Q ss_pred             EEEEeeC
Q 030010           95 KIEIVGT  101 (184)
Q Consensus        95 ~V~~~~~  101 (184)
                      .|...+.
T Consensus       137 ~v~~f~d  143 (698)
T KOG2314|consen  137 FVRLFKD  143 (698)
T ss_pred             Eeehhhh
Confidence            8876543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.89  E-value=6.2e-05  Score=61.46  Aligned_cols=87  Identities=14%  Similarity=0.258  Sum_probs=68.0

Q ss_pred             CCCCCCCCEEEEcCCCC----CCC-------HHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           17 ASAIETGTKLYISNLDY----GVS-------NEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~----~~t-------e~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      ++-....++|.|.||=.    ..+       +++|.+-..+||.|.+|.|...   .+.|.+-|.|.+.++|..||+.|+
T Consensus       259 ~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~  335 (382)
T KOG1548|consen  259 PSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMD  335 (382)
T ss_pred             cccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhc
Confidence            44455568888998821    223       3456677899999999987632   457899999999999999999999


Q ss_pred             CCccCCceEEEEEeeCCCCCC
Q 030010           86 NVQLDGKPMKIEIVGTNIATR  106 (184)
Q Consensus        86 g~~~~g~~i~V~~~~~~~~~~  106 (184)
                      |..|.|++|..++...+....
T Consensus       336 GR~fdgRql~A~i~DG~t~~~  356 (382)
T KOG1548|consen  336 GRWFDGRQLTASIWDGKTKFQ  356 (382)
T ss_pred             CeeecceEEEEEEeCCcceee
Confidence            999999999999987655433

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.87  E-value=7.8e-06  Score=64.13  Aligned_cols=64  Identities=20%  Similarity=0.352  Sum_probs=54.0

Q ss_pred             HHHHHHh-hCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           39 DIKELFS-EVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        39 ~L~~~f~-~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      +|...|+ +||+|+++.|..+..-.-.|-+||.|...++|++|++.||+..+.|++|..++....
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            3444445 899999987776655567889999999999999999999999999999999987654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.79  E-value=7.2e-05  Score=64.49  Aligned_cols=62  Identities=10%  Similarity=0.177  Sum_probs=52.4

Q ss_pred             HHHHHhhCCCeEEEEEEeC-C---CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           40 IKELFSEVGDLKRYSIHYD-R---SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        40 L~~~f~~~G~i~~v~i~~~-~---~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ++..+++||.|..|.|.++ .   ..-..|..||+|.+.+++++|++.|+|..|.++++...+...
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            4555688999999999887 3   233577899999999999999999999999999999888653

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

Probab=97.78  E-value=8.6e-05  Score=44.93  Aligned_cols=52  Identities=21%  Similarity=0.286  Sum_probs=40.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHH
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAV   81 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai   81 (184)
                      +.|-|.+.+....+. +..+|.+||+|..+.+...     ..+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            567888888776544 4558889999999877522     348999999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.60  E-value=5.3e-05  Score=63.39  Aligned_cols=66  Identities=26%  Similarity=0.280  Sum_probs=56.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeC---C---CCC--------cceEEEEEecCHHHHHHHHHHhCC
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD---R---SGR--------SKGTAEVVYSRRADAVAAVKRYNN   86 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~---~---~~~--------~~g~afV~F~~~e~a~~Ai~~l~g   86 (184)
                      .++++|.+.|||..-.-+.|.++|+.+|.|+.|+|+..   .   .+.        .+-+|+|+|...+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46899999999999888999999999999999999876   2   111        145899999999999999998865

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.60  E-value=8.3e-05  Score=58.43  Aligned_cols=72  Identities=21%  Similarity=0.303  Sum_probs=60.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-C--------CCc----ceEEEEEecCHHHHHHHHHHhCCCc
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-S--------GRS----KGTAEVVYSRRADAVAAVKRYNNVQ   88 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~--------~~~----~g~afV~F~~~e~a~~Ai~~l~g~~   88 (184)
                      ..-.||+++||+.+....|+++|++||.|-+|.+-... +        +..    ---++|+|.+...|+.+.+.||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            55789999999999999999999999999988775544 3        121    1245799999999999999999999


Q ss_pred             cCCce
Q 030010           89 LDGKP   93 (184)
Q Consensus        89 ~~g~~   93 (184)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.60  E-value=7.4e-05  Score=65.99  Aligned_cols=84  Identities=10%  Similarity=0.065  Sum_probs=71.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +.+...+.+|||..||..+++.++-++|...-.|+. |.|.+..+++.++.|||+|..++++..|...-+.+.+..+.|+
T Consensus       428 p~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~ir  507 (944)
T KOG4307|consen  428 PFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIR  507 (944)
T ss_pred             CCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEE
Confidence            477788999999999999999999999987666765 7777777888899999999998888888877778888889999


Q ss_pred             EEEee
Q 030010           96 IEIVG  100 (184)
Q Consensus        96 V~~~~  100 (184)
                      |.-..
T Consensus       508 v~si~  512 (944)
T KOG4307|consen  508 VDSIA  512 (944)
T ss_pred             eechh
Confidence            97543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.55  E-value=0.00011  Score=60.82  Aligned_cols=77  Identities=17%  Similarity=0.276  Sum_probs=62.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhC----CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEV----GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~----G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      .-..|.+.+||+++++.++.++|..-    +-.+.|.++...+++..|-|||.|..+++|+.|+.+ |...|..+.|.+.
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHH
Confidence            35677888999999999999999733    234567777767999999999999999999999976 7777777777665


Q ss_pred             Ee
Q 030010           98 IV   99 (184)
Q Consensus        98 ~~   99 (184)
                      .+
T Consensus       239 RS  240 (508)
T KOG1365|consen  239 RS  240 (508)
T ss_pred             HH
Confidence            43

>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1

Probab=97.51  E-value=0.00029  Score=45.63  Aligned_cols=18  Identities=39%  Similarity=0.612  Sum_probs=15.4

Q ss_pred             CCChhhHhHHHHHHhhHH
Q 030010          160 KISAEDLDADLDKYYSEA  177 (184)
Q Consensus       160 ~~~~~~lD~el~~y~~~~  177 (184)
                      ..+...||+|||+||++.
T Consensus        54 ~~~~~~LD~~Ld~Y~~~~   71 (74)
T PF13865_consen   54 SKTKSKLDAELDSYMSKK   71 (74)
T ss_pred             HHHHHHHHHHHHHHHHcc
Confidence            467889999999999954

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.50  E-value=0.00037  Score=59.66  Aligned_cols=68  Identities=16%  Similarity=0.311  Sum_probs=62.3

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHh-hCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHH
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFS-EVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR   83 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~-~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~   83 (184)
                      ...+.++.++|||++||.-++-++|-.+|. .||-|..+-|-+|. -+.++|-+=|+|.+..+..+||++
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            356788999999999999999999999999 79999999999995 778999999999999999999974

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.48  E-value=0.00089  Score=41.70  Aligned_cols=55  Identities=27%  Similarity=0.309  Sum_probs=45.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhC---CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEV---GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY   84 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~---G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l   84 (184)
                      ...|+|.++.. ++.++|+.+|..|   ....+|+++.|.      .|.|.|.+.+.|.+|+..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            46799999964 7889999999998   134678998776      5899999999999999754

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.47  E-value=0.00011  Score=63.71  Aligned_cols=80  Identities=28%  Similarity=0.329  Sum_probs=63.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHh-hCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC---Cc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFS-EVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD---GK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~-~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~---g~   92 (184)
                      |+....++.|||.||-.-.|.-+|+.++. ..|.|...  ++|+   .+..|||.|.+.++|.+.+.+||+..+-   .+
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk---IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK  512 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK---IKSHCYVSYSSVEEAAATREALHNVQWPPSNPK  512 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH---hhcceeEecccHHHHHHHHHHHhccccCCCCCc
Confidence            45777899999999988889999999999 56666554  2232   3558999999999999999999996653   46


Q ss_pred             eEEEEEeeC
Q 030010           93 PMKIEIVGT  101 (184)
Q Consensus        93 ~i~V~~~~~  101 (184)
                      .|.|.|...
T Consensus       513 ~L~adf~~~  521 (718)
T KOG2416|consen  513 HLIADFVRA  521 (718)
T ss_pred             eeEeeecch
Confidence            788877543

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.45  E-value=0.00059  Score=58.45  Aligned_cols=63  Identities=14%  Similarity=0.302  Sum_probs=50.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC--C--CCcce---EEEEEecCHHHHHHHHHHh
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR--S--GRSKG---TAEVVYSRRADAVAAVKRY   84 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~--~--~~~~g---~afV~F~~~e~a~~Ai~~l   84 (184)
                      .-+++|||++||+.++|+.|...|..||.+. |.+....  .  -.++|   |+|+.|+++..++.-|.+.
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            4478999999999999999999999999864 6665322  1  23577   9999999998888766543

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.45  E-value=0.00021  Score=64.65  Aligned_cols=82  Identities=17%  Similarity=0.215  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMKI   96 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V   96 (184)
                      ...+.+.+||++|..|+....|...|..||.|..|.+-..     .-|+||.|++...++.|++.|-+..|.+  +.|.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            5667899999999999999999999999999998776422     3399999999999999999999999986  78999


Q ss_pred             EEeeCCCCC
Q 030010           97 EIVGTNIAT  105 (184)
Q Consensus        97 ~~~~~~~~~  105 (184)
                      .++.+....
T Consensus       526 dla~~~~~~  534 (975)
T KOG0112|consen  526 DLASPPGAT  534 (975)
T ss_pred             ccccCCCCC
Confidence            998876543

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.44  E-value=0.00082  Score=46.05  Aligned_cols=76  Identities=13%  Similarity=0.141  Sum_probs=49.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEE-E-------EeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYS-I-------HYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~-i-------~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ..+.|.|-+.|+. ....|-++|++||.|.+.. +       ...+......+..|.|.++.+|++||. .||..|.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            3456788889887 5577888999999997664 0       000111224489999999999999996 4999999875


Q ss_pred             EE-EEEe
Q 030010           94 MK-IEIV   99 (184)
Q Consensus        94 i~-V~~~   99 (184)
                      |. |.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            53 5554

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

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

Probab=97.38  E-value=0.0015  Score=43.02  Aligned_cols=58  Identities=21%  Similarity=0.243  Sum_probs=45.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN   86 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g   86 (184)
                      ...+..||+ .|.+....||.++|+.||.|. |.++.+.      .|||...+.+.|..++..+..
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT------EEEEEECCCHHHHHHHHHHTT
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC------cEEEEeecHHHHHHHHHHhcc
Confidence            345777777 999999999999999999975 7777554      699999999999999987754

; 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.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.35  E-value=0.00087  Score=48.79  Aligned_cols=58  Identities=21%  Similarity=0.372  Sum_probs=45.1

Q ss_pred             HHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCCC
Q 030010           39 DIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNIA  104 (184)
Q Consensus        39 ~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~~  104 (184)
                      +|-+.|.+||.+.-|+++.+       .-+|+|.+-+.|.+|+. +++.++.|+.|+|.+..+...
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPDWL  109 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE------
T ss_pred             HHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCccHH
Confidence            57778889999988888743       57999999999999995 799999999999999887543

; PDB: 1UFW_A 2DNR_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.34  E-value=0.00017  Score=64.96  Aligned_cols=82  Identities=22%  Similarity=0.295  Sum_probs=73.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ......|+|.|+|+..|.+.|+.++..+|.++.+.++..+.++++|.+||.|.+..++.+++...+...+.-..+.|.+.
T Consensus       733 ~~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vs  812 (881)
T KOG0128|consen  733 FFGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVS  812 (881)
T ss_pred             hhhhhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCcccccc
Confidence            33468899999999999999999999999999999998889999999999999999999999888888887778888886


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      .+
T Consensus       813 np  814 (881)
T KOG0128|consen  813 NP  814 (881)
T ss_pred             CC
Confidence            65

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.28  E-value=0.001  Score=53.49  Aligned_cols=65  Identities=18%  Similarity=0.152  Sum_probs=53.1

Q ss_pred             HHHHHHHHhhCCCeEEEEEEeCCCC--CcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           37 NEDIKELFSEVGDLKRYSIHYDRSG--RSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        37 e~~L~~~f~~~G~i~~v~i~~~~~~--~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ++++++.+.+||+|.+|.|..+.+.  .-..-.||+|+..++|.+|+-.|||..|.|+.+...+..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            3567888999999999988777621  1233579999999999999999999999999988877543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.14  E-value=0.00089  Score=55.70  Aligned_cols=76  Identities=12%  Similarity=0.215  Sum_probs=61.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC----CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR----SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~----~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ..|.|.||.+.++.++++.||.-.|+|..+.|+.+.    -....-.|||-|.+...+..|.. |.+..|-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            489999999999999999999999999999887644    23345689999999999999975 6677777766666544


Q ss_pred             e
Q 030010          100 G  100 (184)
Q Consensus       100 ~  100 (184)
                      .
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            3

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.98  E-value=0.0015  Score=56.69  Aligned_cols=76  Identities=16%  Similarity=0.201  Sum_probs=60.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhh--CCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSE--VGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN--VQLDGK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~--~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g--~~~~g~   92 (184)
                      -.+..+-|.|.|.-||.++-+++++.||..  +-++..|.+-.+.      -.||+|++..+|+.|.+.|..  .+|.|+
T Consensus       169 Vrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgK  242 (684)
T KOG2591|consen  169 VRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGK  242 (684)
T ss_pred             cccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCc
Confidence            345566788999999999999999999974  6678888886543      479999999999999887764  677777


Q ss_pred             eEEEEE
Q 030010           93 PMKIEI   98 (184)
Q Consensus        93 ~i~V~~   98 (184)
                      +|...+
T Consensus       243 pImARI  248 (684)
T KOG2591|consen  243 PIMARI  248 (684)
T ss_pred             chhhhh
Confidence            766554

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.89  E-value=4.5e-05  Score=68.47  Aligned_cols=67  Identities=30%  Similarity=0.391  Sum_probs=57.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      .++||+||+..+.+.+|...|..++.|..+.|.... .++.+|+|||+|..++.+.+||.......+.
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            578999999999999999999999998888777555 7889999999999999999999765544444

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.53  E-value=0.0027  Score=53.45  Aligned_cols=74  Identities=26%  Similarity=0.282  Sum_probs=58.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccCCceEEEEEeeCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN-VQLDGKPMKIEIVGTN  102 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g-~~~~g~~i~V~~~~~~  102 (184)
                      ..+||+||.+.++..+|+.+|...-.-..-.++.     ..+|+||.+.+..-|.+|++.+++ .++.|+++.|+...++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            4689999999999999999997541101111111     256999999999999999999998 8889999999887654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.53  E-value=0.004  Score=49.18  Aligned_cols=62  Identities=26%  Similarity=0.475  Sum_probs=56.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      ..|||.||...++-+.|.+.|+.||+|....++.|..++..+-.+|+|...-.+.+|+....
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            78999999999999999999999999988777778788888899999999999999988764

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.48  E-value=0.0055  Score=46.35  Aligned_cols=72  Identities=18%  Similarity=0.237  Sum_probs=46.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhh-CCCe---EEEEEEeCC--C-CCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSE-VGDL---KRYSIHYDR--S-GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~-~G~i---~~v~i~~~~--~-~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ....+|.|++||+++||+++.+.++. ++..   ..+.-....  . .....-|||.|.+.+++..-+..++++.|.+.
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            45679999999999999998886665 5544   344322222  1 22356799999999999999999999777653

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.45  E-value=0.055  Score=48.81  Aligned_cols=67  Identities=16%  Similarity=0.349  Sum_probs=48.7

Q ss_pred             EEEEcCC--CCCCCHHHHHHHHhhCCCe-----EEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           25 KLYISNL--DYGVSNEDIKELFSEVGDL-----KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        25 ~l~V~nL--p~~~te~~L~~~f~~~G~i-----~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ++|| |+  -..++..+|-.++..-+.|     -.|+|..       .|.||+.. .+.+...+..|++..+.|+.|.|+
T Consensus       488 ~~~~-~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~-------~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~  558 (629)
T PRK11634        488 LYRI-EVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFA-------SHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQ  558 (629)
T ss_pred             EEEE-ecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeC-------CceEEEcC-hhhHHHHHHHhccccccCCceEEE
Confidence            3444 45  3357888888887655544     3455553       38899987 567888899999999999999999


Q ss_pred             Eee
Q 030010           98 IVG  100 (184)
Q Consensus        98 ~~~  100 (184)
                      .+.
T Consensus       559 ~~~  561 (629)
T PRK11634        559 LLG  561 (629)
T ss_pred             ECC
Confidence            875

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.90  E-value=0.0027  Score=51.86  Aligned_cols=80  Identities=18%  Similarity=0.327  Sum_probs=61.1

Q ss_pred             CEEEEcCCCCCCC-HHHHH--HHHhhCCCeEEEEEEeCCC----CCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           24 TKLYISNLDYGVS-NEDIK--ELFSEVGDLKRYSIHYDRS----GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        24 ~~l~V~nLp~~~t-e~~L~--~~f~~~G~i~~v~i~~~~~----~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .-+||-+|+..+. |..|+  +.|.+||.|.+|.+..+.+    .-...-+||+|...++|..||...++..+.++.|+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            5577778877654 44554  5689999999988877552    122335899999999999999999999999998888


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      .+..++.
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            7766543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.78  E-value=0.012  Score=52.18  Aligned_cols=73  Identities=12%  Similarity=0.250  Sum_probs=63.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      .+..+.-+|||+|+...+..+-++.++..+|.|..++...        |+|++|..+.-...|+..++-..+++..+.+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            4455678999999999999999999999999987766542        99999999999999999999999988877765


Q ss_pred             E
Q 030010           98 I   98 (184)
Q Consensus        98 ~   98 (184)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            5

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.73  E-value=0.0023  Score=58.23  Aligned_cols=80  Identities=16%  Similarity=0.194  Sum_probs=67.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..+.+||++||+..+++.+|+..|..+|.|..|.|...+-+.-.-|+||.|.+.+.+-.|+..+.+..|..-.+++-+..
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            34689999999999999999999999999999998776533444599999999999999998888888776666666653

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=95.59  E-value=0.093  Score=33.71  Aligned_cols=59  Identities=20%  Similarity=0.270  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHhhCC-----CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           33 YGVSNEDIKELFSEVG-----DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        33 ~~~te~~L~~~f~~~G-----~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ..++..+|..++...+     .|-.|+|..+       |+||+-.. +.+..++..|++..+.|++++|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3578888888887664     4556777633       89999874 5888999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.20  E-value=0.18  Score=36.65  Aligned_cols=75  Identities=16%  Similarity=0.253  Sum_probs=53.3

Q ss_pred             CCCCCCCEEEEcCCCCCCC-HHH---HHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           18 SAIETGTKLYISNLDYGVS-NED---IKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~t-e~~---L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .-..+-.+|.|.=|..++. .+|   +...++.||+|..|.+.      .+-.|.|.|.+..+|=.|+.+++. ..-|..
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC------GRQSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec------CCceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            3445566777776655543 234   45557899999998774      233799999999999999999876 445666


Q ss_pred             EEEEEe
Q 030010           94 MKIEIV   99 (184)
Q Consensus        94 i~V~~~   99 (184)
                      +.+.|-
T Consensus       154 ~qCsWq  159 (166)
T PF15023_consen  154 FQCSWQ  159 (166)
T ss_pred             EEeecc
Confidence            666654

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.12  E-value=0.014  Score=49.94  Aligned_cols=74  Identities=19%  Similarity=0.338  Sum_probs=58.8

Q ss_pred             CCEEEEcCCCCCC-CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGV-SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~-te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .+.|-+.-+|+.. +.++|..+|.+||.|..|.|-+..     -.|.|+|.+..+|-.|. ..++..|+++.|+|.|.++
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~-----~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS-----LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCch-----hhheeeeeccccccchh-ccccceecCceeEEEEecC
Confidence            3445555566664 468999999999999999886542     26899999999997775 4699999999999999887


Q ss_pred             C
Q 030010          102 N  102 (184)
Q Consensus       102 ~  102 (184)
                      .
T Consensus       446 s  446 (526)
T KOG2135|consen  446 S  446 (526)
T ss_pred             C
Confidence            3

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.89  E-value=0.095  Score=39.92  Aligned_cols=62  Identities=19%  Similarity=0.242  Sum_probs=44.3

Q ss_pred             CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCceEEEEEeeCC
Q 030010           36 SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN--NVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        36 te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~--g~~~~g~~i~V~~~~~~  102 (184)
                      ..+.|+++|..|+.+..+.+..     +-.-..|.|.+.+.|.+|...|+  +..+.+..|+|.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~-----sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK-----SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET-----TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcC-----CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            4578999999999887665542     23358899999999999999999  89999999999988543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.62  E-value=0.0027  Score=53.47  Aligned_cols=80  Identities=19%  Similarity=0.287  Sum_probs=66.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      +..+-|.|+|+...|+.|..|+.+||.++.|..+...+.  .-..-|+|...+.++.||.+|++..+....++|.+....
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e--tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPde  157 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE--TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDE  157 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH--HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchh
Confidence            466889999999999999999999999998876433221  225568899999999999999999999999999987664


Q ss_pred             CC
Q 030010          103 IA  104 (184)
Q Consensus       103 ~~  104 (184)
                      ..
T Consensus       158 q~  159 (584)
T KOG2193|consen  158 QN  159 (584)
T ss_pred             hh
Confidence            44

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.48  E-value=0.17  Score=41.17  Aligned_cols=63  Identities=22%  Similarity=0.303  Sum_probs=45.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .=|-|-++|+. .-..|..+|++||.|.+....  .+   -.+-+|.|.+..+|++||.+ |+..|++..
T Consensus       198 ~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~--~n---gNwMhirYssr~~A~KALsk-ng~ii~g~v  260 (350)
T KOG4285|consen  198 TWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP--SN---GNWMHIRYSSRTHAQKALSK-NGTIIDGDV  260 (350)
T ss_pred             ceEEEeccCcc-chhHHHHHHHhhCeeeeeecC--CC---CceEEEEecchhHHHHhhhh-cCeeeccce
Confidence            33445566654 345678899999998765332  22   33899999999999999975 888888753

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=94.23  E-value=0.083  Score=46.02  Aligned_cols=78  Identities=15%  Similarity=0.113  Sum_probs=48.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHh-hCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC----CceEEEE
Q 030010           24 TKLYISNLDYGVSNEDIKELFS-EVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD----GKPMKIE   97 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~-~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~----g~~i~V~   97 (184)
                      +++-|.|+|...|...|..... ..|.-..+.+..|= +....|||||.|.+++.+..+.+++||+.+.    .+.+.|.
T Consensus       389 tt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~it  468 (549)
T KOG4660|consen  389 TTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASIT  468 (549)
T ss_pred             hhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeee
Confidence            3444444444433333322221 23444556666665 5667899999999999999999999995543    2455666


Q ss_pred             EeeC
Q 030010           98 IVGT  101 (184)
Q Consensus        98 ~~~~  101 (184)
                      |++-
T Consensus       469 YArI  472 (549)
T KOG4660|consen  469 YARI  472 (549)
T ss_pred             hhhh
Confidence            6554

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=93.96  E-value=1.3  Score=30.81  Aligned_cols=68  Identities=10%  Similarity=0.095  Sum_probs=47.7

Q ss_pred             CCEEEEc-CCCCCCCHHHHHHHHhhC-CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           23 GTKLYIS-NLDYGVSNEDIKELFSEV-GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        23 ~~~l~V~-nLp~~~te~~L~~~f~~~-G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      .+.|.|- ..|..++.++|..+.+.+ ..|..++|+++... .+-.+.+.|.+.+.|..-.+.+||..|+-
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3444443 445555666776665554 35677888877632 34578999999999999999999987764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=93.77  E-value=0.45  Score=29.98  Aligned_cols=55  Identities=22%  Similarity=0.276  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           34 GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        34 ~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .++-++|+..|..|.- ..  |..+++     --||.|.+..+|+++....++..+....|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~--I~~d~t-----GfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DR--IRDDRT-----GFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEecCC-----EEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3678999999999953 33  444543     3589999999999999999998888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.39  E-value=0.065  Score=48.95  Aligned_cols=69  Identities=19%  Similarity=0.241  Sum_probs=56.2

Q ss_pred             CCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC--CceEEEEEeeCCC
Q 030010           30 NLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD--GKPMKIEIVGTNI  103 (184)
Q Consensus        30 nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~--g~~i~V~~~~~~~  103 (184)
                      |.+-..+...|..+|++||.|..++..++-     ..|.|+|.+.+.|..|+.+|+|.++.  |-+.+|.+++.-.
T Consensus       305 nn~v~~tSssL~~l~s~yg~v~s~wtlr~~-----N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  305 NNAVNLTSSSLATLCSDYGSVASAWTLRDL-----NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             cccccchHHHHHHHHHhhcchhhheecccc-----cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            344456677899999999999988776553     38999999999999999999996654  7788999888644

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=92.81  E-value=0.075  Score=43.27  Aligned_cols=81  Identities=17%  Similarity=0.203  Sum_probs=62.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ...+++|++++.+.+.+.++..++..+|.+....+.... ....++++++.|...+.+..|+.......+.+..+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            457899999999999999899999999977666665544 6678999999999999999999754434555555555444


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      ..
T Consensus       166 ~~  167 (285)
T KOG4210|consen  166 TR  167 (285)
T ss_pred             cc
Confidence            43

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.52  E-value=1.1  Score=39.58  Aligned_cols=82  Identities=20%  Similarity=0.258  Sum_probs=62.7

Q ss_pred             CCCCCCCCEEEEcCCCCC-CCHHHHHHHHhhC----CCeEEEEEEeCCC-----------CC------------------
Q 030010           17 ASAIETGTKLYISNLDYG-VSNEDIKELFSEV----GDLKRYSIHYDRS-----------GR------------------   62 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~-~te~~L~~~f~~~----G~i~~v~i~~~~~-----------~~------------------   62 (184)
                      +...+.+++|-|.|+.|. +...+|..+|+.|    |.|.+|.|+...-           |.                  
T Consensus       168 ~~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~  247 (650)
T KOG2318|consen  168 PVLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDD  247 (650)
T ss_pred             cccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccch
Confidence            445677899999999997 7789999998876    5888888765321           11                  


Q ss_pred             -------------------cceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           63 -------------------SKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        63 -------------------~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                                         ..=||.|+|.+.+.|.+..+..+|.+|...-..+.+
T Consensus       248 ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DL  302 (650)
T KOG2318|consen  248 EEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDL  302 (650)
T ss_pred             hhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeee
Confidence                               113789999999999999999999999865444443

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=89.88  E-value=1.7  Score=37.38  Aligned_cols=68  Identities=16%  Similarity=0.199  Sum_probs=57.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhC-CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEV-GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~-G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      ++.|+|--+|..++-.||-.|+..+ -.|..++|++|.... +=.+.|.|.+.++|....+.+||..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn-rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN-RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc-eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            7899999999999999999998754 467889999866322 3368999999999999999999988875

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=88.78  E-value=2.4  Score=34.48  Aligned_cols=46  Identities=17%  Similarity=0.205  Sum_probs=35.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCe-EEEEEEeCCCCCcceEEEEEecCH
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDL-KRYSIHYDRSGRSKGTAEVVYSRR   74 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i-~~v~i~~~~~~~~~g~afV~F~~~   74 (184)
                      +-||++||+..+.-.||+..+.+.+.+ .++.|.     -+.+-||+.|.+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk-----g~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK-----GHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEeee-----cCCcceeEecCCc
Confidence            559999999999999999999887654 444443     2356799999653

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.93  E-value=1.6  Score=37.03  Aligned_cols=56  Identities=20%  Similarity=0.143  Sum_probs=46.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCe-EEEEEEeCCCCCcceEEEEEecCHHHHHHHHH
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDL-KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK   82 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i-~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~   82 (184)
                      +-.+.|-|.++|.....+||..+|+.|+.- -.|+|+.+.      .+|..|.+...|..|+-
T Consensus       389 dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt------halaVFss~~~AaeaLt  445 (528)
T KOG4483|consen  389 DLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT------HALAVFSSVNRAAEALT  445 (528)
T ss_pred             cccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc------eeEEeecchHHHHHHhh
Confidence            356899999999999999999999999753 457777554      79999999999999985

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=81.18  E-value=0.34  Score=37.77  Aligned_cols=81  Identities=28%  Similarity=0.339  Sum_probs=64.6

Q ss_pred             CCCCCCCEEEEcC----CCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           18 SAIETGTKLYISN----LDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        18 ~~~~~~~~l~V~n----Lp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ...+...+++.++    |...++++.+.+.|++.+.+..+++..+.+++.+.+.|+++......-.++..+.+.++--++
T Consensus        75 ~~~e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen   75 EEDEEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKK  154 (267)
T ss_pred             ccchhhcccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCCCC
Confidence            3444556777777    777889999999999999999999988888888889999998888888888877776666555


Q ss_pred             EEEEE
Q 030010           94 MKIEI   98 (184)
Q Consensus        94 i~V~~   98 (184)
                      +.+.-
T Consensus       155 ~~~gg  159 (267)
T KOG4454|consen  155 VTIGG  159 (267)
T ss_pred             ccccc
Confidence            55543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	184
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-25
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-25
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		2e-25
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		1e-23
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		2e-22
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		3e-09
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		5e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		6e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		1e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		3e-05
1sxl_A	97	Resonance Assignments And Solution Structure Of The		6e-05
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		8e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		8e-05
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		1e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		2e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		3e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		4e-04
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		5e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		5e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		6e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		6e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		7e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		7e-04

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score =  112 bits (281), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 50/90 (55%), Positives = 68/90 (75%)
Query: 14  AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
            G    +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++ YDRSGRS GTA+V + R
Sbjct: 26  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFER 85
Query: 74  RADAVAAVKRYNNVQLDGKPMKIEIVGTNI 103
           RADA+ A+K+Y  V LDG+PM I++V + I
Sbjct: 86  RADALKAMKQYKGVPLDGRPMDIQLVASQI 115

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score =  112 bits (280), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 50/90 (55%), Positives = 68/90 (75%)
Query: 14  AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
            G    +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++ YDRSGRS GTA+V + R
Sbjct: 26  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFER 85
Query: 74  RADAVAAVKRYNNVQLDGKPMKIEIVGTNI 103
           RADA+ A+K+Y  V LDG+PM I++V + I
Sbjct: 86  RADALKAMKQYKGVPLDGRPMDIQLVASQI 115

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score =  111 bits (278), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 50/90 (55%), Positives = 68/90 (75%)
Query: 14  AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
            G    +ETG KL +SNLD+GVS+ DI+ELF+E G LK+ ++ YDRSGRS GTA+V + R
Sbjct: 79  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFER 138
Query: 74  RADAVAAVKRYNNVQLDGKPMKIEIVGTNI 103
           RADA+ A+K+Y  V LDG+PM I++V + I
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVASQI 168

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score =  105 bits (262), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 46/75 (61%), Positives = 63/75 (84%)
Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+ADA+ A+K+Y
Sbjct: 30  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 85  NNVQLDGKPMKIEIV 99
           N V LDG+PM I++V
Sbjct: 90  NGVPLDGRPMNIQLV 104

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score =  101 bits (252), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 45/75 (60%), Positives = 61/75 (81%)
Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+ADA+ A K+Y
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 85  NNVQLDGKPMKIEIV 99
           N V LDG+P  I++V
Sbjct: 91  NGVPLDGRPXNIQLV 105

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 50/86 (58%), Gaps = 5/86 (5%)
Query: 13 QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYS 72
          QAGR      G+ ++++NLDY V  + +KE+FS  G + R  I  D+ G+S+G   V + 
Sbjct: 10 QAGR-----LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFE 64
Query: 73 RRADAVAAVKRYNNVQLDGKPMKIEI 98
          +  +AV A+  +N   L  +PM +++
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMHVKM 90

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 42/76 (55%)
Query: 20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVA 79
          ++    LY+ NL +  + E I ELFS+ GD+K+  +  D+   + G   V Y  RADA  
Sbjct: 15 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAEN 74
Query: 80 AVKRYNNVQLDGKPMK 95
          A++  N  +LD + ++
Sbjct: 75 AMRYINGTRLDDRIIR 90

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          +++ N+ Y  + E +K++FSEVG +  + + YDR +G+ KG     Y  +  A++A++  
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 85 NNVQLDGKPMKIE 97
          N  +  G+ ++++
Sbjct: 71 NGREFSGRALRVD 83

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR-SKGTAEVVYSRRADAVAAVKRY 84
          +Y+SNL + ++N D+  +FS+ G + + +I  D+  R SKG A +++  +  A    +  
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 85 NNVQLDGKPMKIEI 98
          NN QL G+ +K  I
Sbjct: 79 NNKQLFGRVIKASI 92

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKR 83
           +LY+ +L + ++ + ++ +F   G ++   +  D  +GRSKG   + +S    A  A+++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 84  YNNVQLDGKPMKI 96
            N  +L G+PMK+
Sbjct: 88  LNGFELAGRPMKV 100

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 7/88 (7%)
Query: 9  FPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAE 68
          FP Q+       E    +++ NL+  V  E + ELF + G L + +I  DR G+ K    
Sbjct: 9  FPAQE-------EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGF 61
Query: 69 VVYSRRADAVAAVKRYNNVQLDGKPMKI 96
          V +        A+   N ++L G+P+ +
Sbjct: 62 VCFKHPESVSYAIALLNGIRLYGRPINV 89

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
          T LY++NL   ++++ +  +F + G + + +I  D+ +GR +G A V Y++R +A  A+ 
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 83 RYNNVQLDG--KPMKIEI 98
            NNV  +G  +P+ + +
Sbjct: 74 ALNNVIPEGGSQPLSVRL 91

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 52/96 (54%), Gaps = 12/96 (12%)
Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
           L +SNL Y  + E ++E+F +   +K   +  +++G+SKG A + ++   DA  A+   N
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 86  NVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNG 121
             +++G+ +++E+ G         P  + N G S+G
Sbjct: 75  KREIEGRAIRLELQG---------PRGSPNSGPSSG 101

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
           T LY++NL   ++++ +  +F + G + + +I  D+ +GR +G A V Y++R +A  A+ 
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 83  RYNNVQLDG--KPMKIEI 98
             NNV  +G  +P+ + +
Sbjct: 161 ALNNVIPEGGSQPLSVRL 178

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 43.1 bits (100), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
           T LY++NL   ++++ +  +F + G + + +I  D+ +GR +G A V Y++R +A  A+ 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 83  RYNNVQLDG--KPMKIEI 98
             NNV  +G  +P+ + +
Sbjct: 150 ALNNVIPEGGSQPLSVRL 167

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 20  IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSK-GTAEVVYSRRADAV 78
           ++    LY+ NL +  + E I ELFS+ GD+K+  +  D+  ++  G   V Y  RADA 
Sbjct: 36  LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 79  AAVKRYNNVQLDGKPMKIE 97
            A++  N  +LD + ++ +
Sbjct: 96  NAMRYINGTRLDDRIIRTD 114

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 8/95 (8%)
Query: 12  QQAGRASA-------IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRS 63
           QQ GR S         +    L +  L    +  D++E+FS+ G +   SI YD+ S RS
Sbjct: 28  QQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 87
Query: 64  KGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI 98
           +G A V +    DA  A +R N ++LDG+ ++++ 
Sbjct: 88  RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
           +Y+ N+DYG + +D++  FS  G + R +I  D+ SG  KG A + ++ R    AAV   
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 85  NNVQLDGKPMKIEIVGTNI 103
             V   G+ +K+    TN+
Sbjct: 99  ETV-FRGRTIKVLPKRTNM 116

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          LY+ NLD G+ +E +++ FS  G +    +  +  GRSKG   V +S   +A  AV   N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 86 NVQLDGKPMKIEI 98
             +  KP+ + +
Sbjct: 77 GRIVATKPLYVAL 89

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL+I  L+   + + +K +F + G +    +  DR+ +S+G A + +   ADA  A K  
Sbjct: 9  KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 85 NNVQLDGKPMKIE 97
          N   L GK +K+E
Sbjct: 69 NGKSLHGKAIKVE 81

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L +  L    +  D++E+FS+ G +   SI YD+ S RS+G A V +    DA  A +R 
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 85 NNVQLDGKPMKIEI 98
          N ++LDG+ ++++ 
Sbjct: 78 NGMELDGRRIRVDF 91

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L +  L    +  D++E+FS+ G +   SI YD+ S RS+G A V +    DA  A +R 
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 85 NNVQLDGKPMKIEI 98
          N ++LDG+ ++++ 
Sbjct: 75 NGMELDGRRIRVDF 88

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL++  L+   S +D++ LF   G+++  +I     G SKG A V YS  A+A AA+   
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 85 NNVQ 88
          +  Q
Sbjct: 77 HGSQ 80

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 7/88 (7%)
Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           KL+IS L +  + E+++E+    G +K   +  +R+G+ KG A V Y   + A  AV   
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV--- 75
Query: 85  NNVQLDGKPMKIEIVGTNIATRTAAPAA 112
             +++DG  +K  I+   +A   + P++
Sbjct: 76  --MKMDGMTIKENII--KVAISNSGPSS 99

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY 84
          L +  L    +  D++E+FS+ G +   SI YD+ S RS+G A V +    DA  A +R 
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 85 NNVQLDGKPMKI 96
          N ++LDG+ +++
Sbjct: 78 NGMELDGRRIRV 89

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
          + LY+ +L + ++ + ++ +F   G +    +  D  +GRSKG   + +S    A  A++
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 83 RYNNVQLDGKPMKI 96
          + N  +L G+PM++
Sbjct: 66 QLNGFELAGRPMRV 79

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 2/88 (2%)
Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAVKRY 84
           LY+ NL   V+  D+  LF+   + K   I +   +GR +G A + +  +  A  A+   
Sbjct: 28  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 85  NNVQLDGKPMKIEIVGTNIATRTAAPAA 112
           N  +L GK + IE  G N   R++ P++
Sbjct: 88  NGYKLYGKILVIEF-GKNKKQRSSGPSS 114

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 2/88 (2%)
Query: 13  QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVY 71
           + G   ++E G  L+++ +    + EDI + F+E G++K   ++ D R+G  KG   V Y
Sbjct: 14  EPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Query: 72  SRRADAVAAVKRYNNVQLDGKPMKIEIV 99
               +A AA++  N   L G+P+ ++  
Sbjct: 73  ETYKEAQAAMEGLNGQDLMGQPISVDWC 100

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAV 81
          G  L+++ +    + EDI + F+E G++K   ++ D R+G  KG   V Y    +A AA+
Sbjct: 9  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 82 KRYNNVQLDGKPMKIEIV 99
          +  N   L G+P+ ++  
Sbjct: 69 EGLNGQDLMGQPISVDWC 86

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAV 81
          G  L+++ +    + EDI + F+E G++K   ++ D R+G  KG   V Y    +A AA+
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 82 KRYNNVQLDGKPMKIEIV 99
          +  N   L G+P+ ++  
Sbjct: 67 EGLNGQDLMGQPISVDWC 84

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAV 81
          G  L+++ +    + EDI + F+E G++K   ++ D R+G  KG   V Y    +A AA+
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 82 KRYNNVQLDGKPMKIE 97
          +  N   L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAAV 81
          G  L+++ +    + EDI + F+E G++K   ++ D R+G  KG   V Y    +A AA+
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 82 KRYNNVQLDGKPMKIE 97
          +  N   L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 2/88 (2%)
Query: 13 QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVY 71
          + G   ++E G  L+++ +    + EDI + F+E G++K   ++ D R+G  KG   V Y
Sbjct: 13 EPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 72 SRRADAVAAVKRYNNVQLDGKPMKIEIV 99
              +A AA++  N   L G+P+ ++  
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISVDWC 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.91
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.9
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.9
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.88
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.88
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.88
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.87
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.87
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.87
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.87
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.87
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.87
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.86
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.86
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.86
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.86
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.86
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.86
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.86
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.86
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.86
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.86
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.86
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.86
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.86
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.86
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.86
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.86
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.86
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.85
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.85
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.85
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2div_A	99	TRNA selenocysteine associated protein; structural	99.85
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.85
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.85
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.85
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.85
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.85
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.85
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.85
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.84
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.83
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.83
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.83
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.83
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.83
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.83
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.83
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.83
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.83
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.82
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.82
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.82
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.82
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.82
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.82
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.82
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.81
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.81
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.81
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.81
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.81
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.81
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.81
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.81
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.81
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.8
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.8
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.8
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.8
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.8
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.8
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.8
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.8
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.79
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.79
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.79
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.79
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.79
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.78
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.78
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.77
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.77
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.77
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.77
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.76
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.76
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.76
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.75
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.75
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.75
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.75
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.73
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.73
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.73
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.71
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.71
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.71
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.71
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.71
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.7
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.7
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.68
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.68
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.67
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.66
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.66
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.66
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.65
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.65
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.64
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.63
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.62
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.59
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.59
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.59
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.59
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.58
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.58
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.58
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.56
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.54
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.53
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.49
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.44
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.44
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.28
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.1
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.06
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.63
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.15
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.04
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.98
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.97
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.59
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.33
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.24
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.62
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.32
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.18
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.32
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.56
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	84.28

>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=99.91  E-value=3.8e-25  Score=172.76  Aligned_cols=81  Identities=26%  Similarity=0.368  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCC--CeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVG--DLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G--~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++|||+|||+++++++|+++|++||  .|+.|+|+.++ +++++|||||+|.+.++|++||+.||+..|.++.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            568899999999999999999999999  99999999998 999999999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +++.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8754

>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=99.90  E-value=3.8e-23  Score=141.35  Aligned_cols=81  Identities=26%  Similarity=0.463  Sum_probs=77.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ..+++|||+|||+++|+++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|++||+.||+..|.|++|+|+++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>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=99.90  E-value=6.8e-23  Score=150.71  Aligned_cols=86  Identities=29%  Similarity=0.437  Sum_probs=80.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            444578999999999999999999999999999999999998 7899999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      +++++..
T Consensus       114 ~~a~~~~  120 (156)
T 1h2v_Z          114 DWDAGFK  120 (156)
T ss_dssp             EEESCCC
T ss_pred             EECCCCC
Confidence            9998643

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=1.8e-21  Score=135.64  Aligned_cols=90  Identities=29%  Similarity=0.510  Sum_probs=82.8

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ......+.++|||+|||+++++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.++.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A            8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEE
Confidence            34556778999999999999999999999999999999999999889999999999999999999999999999999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |+++......
T Consensus        88 v~~a~~~~~~   97 (114)
T 2do0_A           88 VKMDERALPK   97 (114)
T ss_dssp             EEECSCCCCC
T ss_pred             EEEcccCCCC
Confidence            9998765443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.88  E-value=2.4e-21  Score=135.29  Aligned_cols=92  Identities=21%  Similarity=0.359  Sum_probs=84.6

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .......+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (115)
T 2dgo_A            7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ   86 (115)
T ss_dssp             SSCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             cCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            345566778999999999999999999999999999999999997 8999999999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCC
Q 030010           94 MKIEIVGTNIATR  106 (184)
Q Consensus        94 i~V~~~~~~~~~~  106 (184)
                      |+|+++.+.....
T Consensus        87 l~V~~a~~~~~~~   99 (115)
T 2dgo_A           87 IRTNWATRKPPAP   99 (115)
T ss_dssp             CEEEESSCCCCCS
T ss_pred             EEEEEccCCCCCC
Confidence            9999998765543

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

Probab=99.88  E-value=6.6e-22  Score=137.71  Aligned_cols=82  Identities=15%  Similarity=0.221  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|+++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            457899999999999999999999999999999999998 7999999999999999999999999999999999999998


Q ss_pred             eCC
Q 030010          100 GTN  102 (184)
Q Consensus       100 ~~~  102 (184)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.88  E-value=1e-21  Score=137.26  Aligned_cols=91  Identities=21%  Similarity=0.341  Sum_probs=83.3

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+....+.++|||+|||+++++++|+++|++||.|..|+|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|
T Consensus        18 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           18 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             CCCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34555677999999999999999999999999999999999998 89999999999999999999999999999999999


Q ss_pred             EEEEeeCCCCCC
Q 030010           95 KIEIVGTNIATR  106 (184)
Q Consensus        95 ~V~~~~~~~~~~  106 (184)
                      +|++++++....
T Consensus        98 ~V~~a~~~~~~~  109 (115)
T 2cpz_A           98 KVQLKRSKNDSK  109 (115)
T ss_dssp             EEECCCCSCCCC
T ss_pred             EEEEcCCCCcCC
Confidence            999998765433

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.4e-21  Score=133.59  Aligned_cols=90  Identities=22%  Similarity=0.467  Sum_probs=83.0

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      +......+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.
T Consensus         4 ~~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 1x5s_A            4 GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQ   83 (102)
T ss_dssp             SCCCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCC
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            345566778999999999999999999999999999999999988 8889999999999999999999999999999999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      |+|+++++...
T Consensus        84 l~v~~a~~~~~   94 (102)
T 1x5s_A           84 IRVDQAGKSSD   94 (102)
T ss_dssp             CEEEEEECCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987554

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=1.9e-21  Score=132.35  Aligned_cols=88  Identities=15%  Similarity=0.309  Sum_probs=81.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .+...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+ ||+..|.|+.|+
T Consensus         4 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~   82 (99)
T 2dgs_A            4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVE   82 (99)
T ss_dssp             CCCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEE
Confidence            4556678999999999999999999999999999999999998 78999999999999999999998 999999999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |+++.++...
T Consensus        83 V~~a~~~~~~   92 (99)
T 2dgs_A           83 VKRAEPRDSK   92 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCccc
Confidence            9999865543

>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=99.87  E-value=1.7e-21  Score=132.51  Aligned_cols=88  Identities=25%  Similarity=0.360  Sum_probs=81.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      +...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (99)
T 1whw_A            3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV   82 (99)
T ss_dssp             CCCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            345678999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q 030010           97 EIVGTNIAT  105 (184)
Q Consensus        97 ~~~~~~~~~  105 (184)
                      +++.+....
T Consensus        83 ~~a~~~~~~   91 (99)
T 1whw_A           83 LPSTIKKEA   91 (99)
T ss_dssp             EECCCCSTT
T ss_pred             EEcCCCccc
Confidence            999876553

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=1e-21  Score=134.69  Aligned_cols=90  Identities=20%  Similarity=0.363  Sum_probs=83.1

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .++...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL   85 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCC
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            45566778999999999999999999999999999999999988 78999999999999999999999999999999999


Q ss_pred             EEEEeeCCCCC
Q 030010           95 KIEIVGTNIAT  105 (184)
Q Consensus        95 ~V~~~~~~~~~  105 (184)
                      +|++++.....
T Consensus        86 ~V~~a~~~~~~   96 (103)
T 2dnm_A           86 RVQVARYGRRD   96 (103)
T ss_dssp             EEEECSSCCSC
T ss_pred             EEEECCcCCCC
Confidence            99999865443

>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=99.87  E-value=2e-21  Score=133.51  Aligned_cols=91  Identities=26%  Similarity=0.400  Sum_probs=83.7

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ...+....+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (105)
T 1x5u_A            6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   85 (105)
T ss_dssp             SCCCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CCCcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            3445666788999999999999999999999999999999999998 899999999999999999999999999999999


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      .|+|+++.+...
T Consensus        86 ~l~v~~a~~~~~   97 (105)
T 1x5u_A           86 PIRVNKASAHNK   97 (105)
T ss_dssp             BCEEEETTTTSC
T ss_pred             EEEEEECCCCCc
Confidence            999999976543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=3.3e-21  Score=134.87  Aligned_cols=90  Identities=24%  Similarity=0.389  Sum_probs=81.9

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      +..+....+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.+++ .|.++
T Consensus         8 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~   86 (116)
T 2cqd_A            8 MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGR   86 (116)
T ss_dssp             CCCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTE
T ss_pred             CCCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCE
Confidence            3445666778999999999999999999999999999999999998 889999999999999999999999998 89999


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      .|+|+++.....
T Consensus        87 ~l~V~~a~~~~~   98 (116)
T 2cqd_A           87 KANVNLAYLGAK   98 (116)
T ss_dssp             ECEEEESTTTCC
T ss_pred             EEEEEEcccCCC
Confidence            999999976443

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=3.1e-21  Score=130.18  Aligned_cols=84  Identities=24%  Similarity=0.511  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++++|||+|||..+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            3568999999999999999999999999999999999998 789999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +.++.
T Consensus        82 a~~~~   86 (95)
T 2dnz_A           82 VTERL   86 (95)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            97643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=2.2e-21  Score=132.97  Aligned_cols=89  Identities=24%  Similarity=0.397  Sum_probs=82.7

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ......+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (103)
T 2cq0_A            8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   87 (103)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            34556778999999999999999999999999999999999997 89999999999999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      +|+++.+...
T Consensus        88 ~v~~a~~~~~   97 (103)
T 2cq0_A           88 NVEWAKPSTN   97 (103)
T ss_dssp             EEEESSCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987544

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

Probab=99.86  E-value=4.5e-21  Score=130.71  Aligned_cols=88  Identities=26%  Similarity=0.440  Sum_probs=82.0

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            44556678999999999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |+++.++.
T Consensus        90 v~~a~~~~   97 (100)
T 2do4_A           90 VAISNSGP   97 (100)
T ss_dssp             EEECCCCS
T ss_pred             EEECCCCC
Confidence            99998644

>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=99.86  E-value=2.2e-21  Score=128.74  Aligned_cols=83  Identities=18%  Similarity=0.343  Sum_probs=76.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|++.||+..|.|+.|+|++
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            4568899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      ++++
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            9764

>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=99.86  E-value=1.6e-21  Score=138.34  Aligned_cols=89  Identities=26%  Similarity=0.408  Sum_probs=82.3

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus        15 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            35566678999999999999999999999999999999999998 89999999999999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      +|+++.+...
T Consensus        95 ~v~~a~~~~~  104 (126)
T 3ex7_B           95 SVDWCFVRGP  104 (126)
T ss_dssp             EEEESEESSS
T ss_pred             EEEEecCCCC
Confidence            9999986543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.4e-21  Score=133.69  Aligned_cols=90  Identities=22%  Similarity=0.351  Sum_probs=82.5

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|
T Consensus         5 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 2cqb_A            5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   84 (102)
T ss_dssp             SSCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cCCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34455678999999999999999999999999999999999987 88999999999999999999999999999999999


Q ss_pred             EEEEeeCCCCC
Q 030010           95 KIEIVGTNIAT  105 (184)
Q Consensus        95 ~V~~~~~~~~~  105 (184)
                      +|+++++....
T Consensus        85 ~V~~a~~~~~~   95 (102)
T 2cqb_A           85 RVNLAKPMRIK   95 (102)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999875543

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

Probab=99.86  E-value=1.7e-21  Score=136.67  Aligned_cols=84  Identities=21%  Similarity=0.311  Sum_probs=78.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +....+.++|||+|||+++++++|+++|++||.|..|+|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        34 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             SCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4556678999999999999999999999999999999999987 889999999999999999999999999999999999


Q ss_pred             EEEee
Q 030010           96 IEIVG  100 (184)
Q Consensus        96 V~~~~  100 (184)
                      |++++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99874

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.86  E-value=4e-21  Score=130.80  Aligned_cols=87  Identities=22%  Similarity=0.466  Sum_probs=80.7

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE--------EEEEeCC-CCCcceEEEEEecCHHHHHHHHHHh
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKR--------YSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRY   84 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~--------v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l   84 (184)
                      ...+.+..+.++|||+|||+++++++|+++|++||.|..        |.|+.++ +++++|||||+|.+.++|++||+.|
T Consensus         4 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l   83 (99)
T 2la6_A            4 HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWF   83 (99)
T ss_dssp             SCSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHh
Confidence            344566677899999999999999999999999999999        9999997 8999999999999999999999999


Q ss_pred             CCCccCCceEEEEEee
Q 030010           85 NNVQLDGKPMKIEIVG  100 (184)
Q Consensus        85 ~g~~~~g~~i~V~~~~  100 (184)
                      |+..|.|+.|+|++++
T Consensus        84 ~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           84 DGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             TTCBSSSSBCEEEECC
T ss_pred             CCCEeCCcEEEEEecC
Confidence            9999999999999874

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=5.8e-21  Score=130.86  Aligned_cols=89  Identities=26%  Similarity=0.413  Sum_probs=82.1

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.+ ++++++||||+|.+.++|++||+.||+..|.++.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3455667899999999999999999999999999999999998 889999999999999999999999999999999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |+++.+....
T Consensus        87 V~~a~~~~~~   96 (103)
T 2d9p_A           87 VALAQRKEER   96 (103)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEecccccC
Confidence            9999875543

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

Probab=99.86  E-value=3.7e-21  Score=132.42  Aligned_cols=88  Identities=26%  Similarity=0.411  Sum_probs=81.8

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+....++++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus        16 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   95 (106)
T 1p27_B           16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   95 (106)
T ss_dssp             CBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            44555678999999999999999999999999999999999998 79999999999999999999999999999999999


Q ss_pred             EEEEeeCCC
Q 030010           95 KIEIVGTNI  103 (184)
Q Consensus        95 ~V~~~~~~~  103 (184)
                      +|+++.++.
T Consensus        96 ~V~~a~~~~  104 (106)
T 1p27_B           96 SVDWCFVRG  104 (106)
T ss_dssp             EEEESEESS
T ss_pred             EEEeecCCC
Confidence            999998754

>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=99.86  E-value=1e-20  Score=129.68  Aligned_cols=92  Identities=22%  Similarity=0.458  Sum_probs=82.8

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      +..+....+.++|||+|||+++++++|+++|++||.|..|.|+.++.. +++||||+|.+.++|++||+.||+..|.|+.
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   84 (103)
T 2cq3_A            6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRK   84 (103)
T ss_dssp             CCCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            344566777899999999999999999999999999999999988754 7899999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCC
Q 030010           94 MKIEIVGTNIATR  106 (184)
Q Consensus        94 i~V~~~~~~~~~~  106 (184)
                      |+|+++.++....
T Consensus        85 l~v~~a~~~~~~~   97 (103)
T 2cq3_A           85 IEVNNATARVMTN   97 (103)
T ss_dssp             CEEEECCSSCCCC
T ss_pred             EEEEEcccCCCCC
Confidence            9999998765543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.1e-21  Score=130.13  Aligned_cols=88  Identities=30%  Similarity=0.445  Sum_probs=81.5

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ........+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++
T Consensus         6 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (95)
T 2cqc_A            6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   85 (95)
T ss_dssp             CCCCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3445666778999999999999999999999999999999999998 789999999999999999999999999999999


Q ss_pred             eEEEEEeeC
Q 030010           93 PMKIEIVGT  101 (184)
Q Consensus        93 ~i~V~~~~~  101 (184)
                      .|+|++++.
T Consensus        86 ~l~v~~a~~   94 (95)
T 2cqc_A           86 RIRVSGPSS   94 (95)
T ss_dssp             EEEEECCSC
T ss_pred             EEEEEecCC
Confidence            999999864

>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=99.86  E-value=8.8e-21  Score=130.31  Aligned_cols=87  Identities=24%  Similarity=0.333  Sum_probs=80.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC---ceEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG---KPMK   95 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g---~~i~   95 (184)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.+   +.|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3456899999999999999999999999999999999999999999999999999999999999999999998   9999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |.++.+....
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999876543

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.86  E-value=4.3e-21  Score=132.29  Aligned_cols=85  Identities=58%  Similarity=0.979  Sum_probs=80.0

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .+....+.++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        22 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           22 GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             --CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            46677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEee
Q 030010           96 IEIVG  100 (184)
Q Consensus        96 V~~~~  100 (184)
                      |+++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99985

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.86  E-value=2.3e-21  Score=130.80  Aligned_cols=88  Identities=24%  Similarity=0.387  Sum_probs=79.2

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      +..+....+.++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.|+.
T Consensus         7 ~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (95)
T 2ywk_A            7 GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRP   86 (95)
T ss_dssp             -----CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCE
Confidence            33456667789999999999999999999999999999999999988899999999999999999999999999999999


Q ss_pred             EEEEEeeC
Q 030010           94 MKIEIVGT  101 (184)
Q Consensus        94 i~V~~~~~  101 (184)
                      |+|++++.
T Consensus        87 l~V~~a~~   94 (95)
T 2ywk_A           87 INVSGPSS   94 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999863

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

Probab=99.86  E-value=7.5e-21  Score=130.38  Aligned_cols=89  Identities=18%  Similarity=0.397  Sum_probs=81.6

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ...+.+..+.++|||+|||+++++++|+++|++|| |..|.|+.++ ++++++||||+|.+.++|++|| .||+..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~   83 (103)
T 2dng_A            6 SGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDR   83 (103)
T ss_dssp             CCCCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCe
Confidence            44566677889999999999999999999999996 9999999998 7999999999999999999999 8999999999


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      .|+|+++.+...
T Consensus        84 ~l~V~~a~~~~~   95 (103)
T 2dng_A           84 SLRVDIAEGRKQ   95 (103)
T ss_dssp             ECEEEECCCCCC
T ss_pred             EEEEEEecCCCC
Confidence            999999986443

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=3.2e-21  Score=129.86  Aligned_cols=87  Identities=26%  Similarity=0.445  Sum_probs=80.2

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      +.......+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+
T Consensus         7 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   86 (94)
T 2e5h_A            7 GMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGR   86 (94)
T ss_dssp             CCCCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            3345556678999999999999999999999999999999999988 788999999999999999999999999999999


Q ss_pred             eEEEEEee
Q 030010           93 PMKIEIVG  100 (184)
Q Consensus        93 ~i~V~~~~  100 (184)
                      .|+|++++
T Consensus        87 ~l~v~~ak   94 (94)
T 2e5h_A           87 VIKASIAI   94 (94)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEecC
Confidence            99999974

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=8.3e-21  Score=130.77  Aligned_cols=90  Identities=22%  Similarity=0.430  Sum_probs=82.8

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeC-C-CCCcceEEEEEecCHHHHHHHHHHh-CCCccCCc
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-R-SGRSKGTAEVVYSRRADAVAAVKRY-NNVQLDGK   92 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~-~-~~~~~g~afV~F~~~e~a~~Ai~~l-~g~~~~g~   92 (184)
                      .+....+.++|||+|||+++++++|+++|++||.|..|.|+.+ + ++++++||||+|.+.++|++||+.| |+..|.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A            8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             ccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            4556677899999999999999999999999999999999998 5 8899999999999999999999999 99999999


Q ss_pred             eEEEEEeeCCCCC
Q 030010           93 PMKIEIVGTNIAT  105 (184)
Q Consensus        93 ~i~V~~~~~~~~~  105 (184)
                      .|+|+++.+....
T Consensus        88 ~l~v~~a~~~~~~  100 (107)
T 2cph_A           88 RLVLEWADSEVTV  100 (107)
T ss_dssp             BCEEEECCCCCCC
T ss_pred             EEEEEeCCCCCCC
Confidence            9999999875543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.86  E-value=1.3e-20  Score=135.72  Aligned_cols=86  Identities=19%  Similarity=0.321  Sum_probs=80.0

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||.++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345567999999999999999999999999999999999998 7899999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      +++++..
T Consensus       117 ~~a~~~~  123 (139)
T 1u6f_A          117 ALAASGH  123 (139)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9998643

>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=99.86  E-value=2.4e-21  Score=138.51  Aligned_cols=90  Identities=30%  Similarity=0.444  Sum_probs=83.1

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ........+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+
T Consensus        37 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~  116 (129)
T 2kxn_B           37 VGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR  116 (129)
T ss_dssp             CCCSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3345667788999999999999999999999999999999999998 789999999999999999999999999999999


Q ss_pred             eEEEEEeeCCC
Q 030010           93 PMKIEIVGTNI  103 (184)
Q Consensus        93 ~i~V~~~~~~~  103 (184)
                      .|+|+++.++.
T Consensus       117 ~l~V~~a~~~~  127 (129)
T 2kxn_B          117 RIRVDFSITKR  127 (129)
T ss_dssp             CCEESCCSSSS
T ss_pred             EEEEEEecCCC
Confidence            99999998654

>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=99.86  E-value=1.3e-20  Score=132.29  Aligned_cols=85  Identities=27%  Similarity=0.413  Sum_probs=79.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++.++|||+|||+++++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34668999999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +++..
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98644

>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=99.86  E-value=7.1e-21  Score=125.24  Aligned_cols=80  Identities=21%  Similarity=0.448  Sum_probs=76.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      +++|||+|||..+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|++.||+..|.|+.|+|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            4689999999999999999999999999999999997 899999999999999999999999999999999999999986


Q ss_pred             C
Q 030010          102 N  102 (184)
Q Consensus       102 ~  102 (184)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.86  E-value=7.9e-21  Score=131.72  Aligned_cols=90  Identities=23%  Similarity=0.416  Sum_probs=82.9

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhC------CCc
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN------NVQ   88 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~------g~~   88 (184)
                      .+....+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||      +..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A            8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            34566778999999999999999999999999999999999998 78999999999999999999999999      999


Q ss_pred             cCCceEEEEEeeCCCCC
Q 030010           89 LDGKPMKIEIVGTNIAT  105 (184)
Q Consensus        89 ~~g~~i~V~~~~~~~~~  105 (184)
                      |.|+.|+|.++.++...
T Consensus        88 ~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           88 LDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SSSCEEEEECCCCCCCC
T ss_pred             EcCEEEEEEECCCCccC
Confidence            99999999999875543

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

Probab=99.85  E-value=7.4e-21  Score=130.47  Aligned_cols=88  Identities=17%  Similarity=0.294  Sum_probs=81.5

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhh-CCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc-cCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSE-VGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQ-LDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~-~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~-~~g~~i   94 (184)
                      .....+.++|||+|||+++++++|+++|++ ||.|..|.|+.++++++++||||+|.+.++|++||+.||+.. |.|+.|
T Consensus         3 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l   82 (104)
T 2dhg_A            3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV   82 (104)
T ss_dssp             CCCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCC
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeE
Confidence            345567899999999999999999999999 999999999999988999999999999999999999999999 999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      +|+++.+...
T Consensus        83 ~v~~a~~~~~   92 (104)
T 2dhg_A           83 RLSVAIPKAS   92 (104)
T ss_dssp             CCCBCCCCCS
T ss_pred             EEEEccCCCc
Confidence            9999876544

>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=99.85  E-value=3.1e-21  Score=127.54  Aligned_cols=82  Identities=24%  Similarity=0.400  Sum_probs=77.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|++.||+..|.|+.|+|+
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45678999999999999999999999999999999999886 88899999999999999999999999999999999999


Q ss_pred             Eee
Q 030010           98 IVG  100 (184)
Q Consensus        98 ~~~  100 (184)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            874

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=5.1e-22  Score=133.65  Aligned_cols=82  Identities=17%  Similarity=0.287  Sum_probs=75.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCC-CeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhC-CCccCCceEEEEEe
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVG-DLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN-NVQLDGKPMKIEIV   99 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G-~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~-g~~~~g~~i~V~~~   99 (184)
                      +.+|||+|||+++||++|+++|++|| .|..|+|+.++ +++++|||||+|.+.++|++||+.++ +..|.|++|+|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            57899999999999999999999999 89999999998 89999999999999999999999875 57899999999999


Q ss_pred             eCCCC
Q 030010          100 GTNIA  104 (184)
Q Consensus       100 ~~~~~  104 (184)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.85  E-value=1e-20  Score=129.73  Aligned_cols=85  Identities=25%  Similarity=0.362  Sum_probs=77.1

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      +..+....+.++|||+|||+.+++++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|.++.
T Consensus         2 s~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   74 (103)
T 2dgu_A            2 SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGEN   74 (103)
T ss_dssp             CCCCCCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCE
Confidence            4456677788999999999999999999999999999999987       459999999999999999999999999999


Q ss_pred             EEEEEeeCCCCC
Q 030010           94 MKIEIVGTNIAT  105 (184)
Q Consensus        94 i~V~~~~~~~~~  105 (184)
                      |+|+++++....
T Consensus        75 l~v~~a~~~~~~   86 (103)
T 2dgu_A           75 IEIVFAKPPDQK   86 (103)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEcCCCccc
Confidence            999999875543

>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=99.85  E-value=6.8e-21  Score=131.08  Aligned_cols=88  Identities=23%  Similarity=0.414  Sum_probs=80.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCcc---CCc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQL---DGK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~---~g~   92 (184)
                      +....+.++|||+|||.++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..+   .++
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            4456678999999999999999999999999999999999988 799999999999999999999999999887   889


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      .|+|.++.+...
T Consensus        87 ~l~v~~a~~~~~   98 (106)
T 2dgp_A           87 PIQVKPADSESR   98 (106)
T ss_dssp             CCEEEECCCCSC
T ss_pred             eEEEEECCcccc
Confidence            999999986543

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

Probab=99.85  E-value=8.9e-21  Score=127.19  Aligned_cols=87  Identities=22%  Similarity=0.395  Sum_probs=79.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      +++..+.++|||+|||+++++++|+++|++||.|..|.|+.+ ++++++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         2 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   80 (92)
T 2dgv_A            2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDV   80 (92)
T ss_dssp             CCSSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCC
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            345567899999999999999999999999999999999874 7788999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      +++++...
T Consensus        81 ~~a~~~~~   88 (92)
T 2dgv_A           81 RIDRNASG   88 (92)
T ss_dssp             EECSCCSS
T ss_pred             EEcCCCCC
Confidence            99986543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=5.9e-21  Score=129.84  Aligned_cols=86  Identities=19%  Similarity=0.271  Sum_probs=79.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE-EEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce--
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLK-RYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP--   93 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~-~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~--   93 (184)
                      ....+.++|||+|||+++++++|+++|++||.|. .|+|+.++ ++++++||||+|.+.++|++||+.||+..|.++.  
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            4456789999999999999999999999999999 99999998 8999999999999999999999999999999999  


Q ss_pred             --EEEEEeeCCC
Q 030010           94 --MKIEIVGTNI  103 (184)
Q Consensus        94 --i~V~~~~~~~  103 (184)
                        |+|+++++..
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence              9999987543

>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=99.85  E-value=1.7e-20  Score=158.88  Aligned_cols=85  Identities=20%  Similarity=0.443  Sum_probs=79.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..+.++|||+|||+.||+++|+.+|++||.|+.|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             eeCCCC
Q 030010           99 VGTNIA  104 (184)
Q Consensus        99 ~~~~~~  104 (184)
                      +.+...
T Consensus       179 a~~~~~  184 (437)
T 3pgw_S          179 ERGRTV  184 (437)
T ss_pred             eCCCCC
Confidence            986544

>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=99.85  E-value=1.1e-21  Score=131.55  Aligned_cols=82  Identities=24%  Similarity=0.319  Sum_probs=71.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCC--CeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVG--DLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G--~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .+|||+|||+++++++|+++|++||  .|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999998 89999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 030010          101 TNIAT  105 (184)
Q Consensus       101 ~~~~~  105 (184)
                      +....
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76544

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=7.2e-21  Score=132.49  Aligned_cols=88  Identities=24%  Similarity=0.472  Sum_probs=81.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE--------EEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLK--------RYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNV   87 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~--------~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~   87 (184)
                      +....+.++|||+|||+.+++++|+++|++||.|.        .|.|+.++ ++++++||||+|.+.++|++||+.||+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            44566789999999999999999999999999998        69999996 8999999999999999999999999999


Q ss_pred             ccCCceEEEEEeeCCCC
Q 030010           88 QLDGKPMKIEIVGTNIA  104 (184)
Q Consensus        88 ~~~g~~i~V~~~~~~~~  104 (184)
                      .|.|+.|+|+++++...
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            99999999999986544

>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=99.85  E-value=1.7e-20  Score=129.87  Aligned_cols=83  Identities=23%  Similarity=0.384  Sum_probs=75.8

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC---
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG---   91 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g---   91 (184)
                      ..+++....++|||+|||+++++++|+++|++||.|..|.|+.+      +||||+|.+.++|++||+.||+..|.+   
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~   80 (108)
T 1x4c_A            7 GGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   80 (108)
T ss_dssp             SSCCCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTS
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcC
Confidence            34566677999999999999999999999999999999999865      799999999999999999999999999   


Q ss_pred             --ceEEEEEeeCCC
Q 030010           92 --KPMKIEIVGTNI  103 (184)
Q Consensus        92 --~~i~V~~~~~~~  103 (184)
                        +.|+|+++.+..
T Consensus        81 ~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           81 ETAYIRVKVDGPRS   94 (108)
T ss_dssp             CEEEEEEEESSCCS
T ss_pred             cceEEEEEeCCCCC
Confidence              999999998643

>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=99.85  E-value=2.5e-20  Score=127.62  Aligned_cols=88  Identities=24%  Similarity=0.290  Sum_probs=79.8

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.++.. .++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   86 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEE
Confidence            4556677899999999999999999999999999999999988633 588999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q 030010           96 IEIVGTNIA  104 (184)
Q Consensus        96 V~~~~~~~~  104 (184)
                      |++++++..
T Consensus        87 V~~a~~~~~   95 (103)
T 2cqi_A           87 VNWATTPSS   95 (103)
T ss_dssp             EEECCCTTC
T ss_pred             EEECCCCcc
Confidence            999987543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.85  E-value=1.6e-20  Score=133.00  Aligned_cols=93  Identities=54%  Similarity=0.919  Sum_probs=85.4

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ...+...++++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus        27 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  106 (124)
T 2kt5_A           27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  106 (124)
T ss_dssp             CCCCCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            34456778899999999999999999999999999999999999888999999999999999999999999999999999


Q ss_pred             EEEEeeCCCCCCC
Q 030010           95 KIEIVGTNIATRT  107 (184)
Q Consensus        95 ~V~~~~~~~~~~~  107 (184)
                      +|+++.+.....+
T Consensus       107 ~V~~a~~~~~~~~  119 (124)
T 2kt5_A          107 DIQLVASQIDLEH  119 (124)
T ss_dssp             EEEEECCTTCCCC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999988665544

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=5.2e-21  Score=129.30  Aligned_cols=84  Identities=23%  Similarity=0.319  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEE-EEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRY-SIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v-~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .++++|||+|||+++++++|+++|++||.|..| .|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            468999999999999999999999999999999 999986 889999999999999999999999999999999999999


Q ss_pred             eeCCCC
Q 030010           99 VGTNIA  104 (184)
Q Consensus        99 ~~~~~~  104 (184)
                      +.+...
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            986443

>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=99.85  E-value=9e-21  Score=128.36  Aligned_cols=84  Identities=25%  Similarity=0.418  Sum_probs=79.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ++++|||+|||..+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+|+++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            57899999999999999999999999999999999998 78999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 030010          101 TNIAT  105 (184)
Q Consensus       101 ~~~~~  105 (184)
                      +....
T Consensus        81 ~~~~~   85 (96)
T 2x1f_A           81 NSDIS   85 (96)
T ss_dssp             CSSGG
T ss_pred             CCCCC
Confidence            76543

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.3e-20  Score=128.40  Aligned_cols=93  Identities=19%  Similarity=0.284  Sum_probs=81.1

Q ss_pred             CCCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 030010            9 FPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQ   88 (184)
Q Consensus         9 ~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~   88 (184)
                      .+......+....+.++|||+|||+++++++|+++|++||.|..|.|..  ++.+++||||+|.+.++|++||+.||+..
T Consensus         8 ~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~   85 (109)
T 1x4a_A            8 MSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYD   85 (109)
T ss_dssp             CCCCCCSSCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCE
T ss_pred             cCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCE
Confidence            3444445566777889999999999999999999999999999999854  34578999999999999999999999999


Q ss_pred             cCCceEEEEEeeCCC
Q 030010           89 LDGKPMKIEIVGTNI  103 (184)
Q Consensus        89 ~~g~~i~V~~~~~~~  103 (184)
                      |.++.|+|+++++..
T Consensus        86 ~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           86 YDGYRLRVEFPRSGR  100 (109)
T ss_dssp             ETTEECEEECCCCCC
T ss_pred             ECCeEEEEEEcccCC
Confidence            999999999987643

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

Probab=99.85  E-value=6.8e-21  Score=140.41  Aligned_cols=81  Identities=17%  Similarity=0.365  Sum_probs=76.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCC--CeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVG--DLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G--~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++|||+|||+++++++|+++|++||  .|..|+|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  99999999998 899999999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +.+.
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8753

>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=99.85  E-value=1e-20  Score=128.29  Aligned_cols=86  Identities=20%  Similarity=0.333  Sum_probs=77.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHH----HHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIK----ELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~----~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ..+....++|||+|||+.+++++|+    ++|++||.|..|.|+.++..  ++||||+|.+.++|++||+.||+..|.|+
T Consensus         3 s~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr   80 (96)
T 2dgx_A            3 SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSK   80 (96)
T ss_dssp             CCCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            3455678999999999999999999    99999999999999988844  78999999999999999999999999999


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      .|+|+++++...
T Consensus        81 ~l~V~~a~~~~~   92 (96)
T 2dgx_A           81 KILVSLATGASG   92 (96)
T ss_dssp             EEEEEECCCSSC
T ss_pred             EEEEEEcCCCCC
Confidence            999999976443

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

Probab=99.85  E-value=2.4e-21  Score=131.50  Aligned_cols=84  Identities=15%  Similarity=0.242  Sum_probs=76.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCC--eEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCC----ccC
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGD--LKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNV----QLD   90 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~--i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~----~~~   90 (184)
                      .....-.+|||+|||+++|+++|+++|++||.  |..|+|+.|+ +++++|||||+|.+.++|++||+.||+.    .|+
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~   83 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            34455678999999999999999999999995  5789999998 8999999999999999999999999996    489


Q ss_pred             CceEEEEEeeC
Q 030010           91 GKPMKIEIVGT  101 (184)
Q Consensus        91 g~~i~V~~~~~  101 (184)
                      |++|.|++++.
T Consensus        84 Gr~i~V~~Aks   94 (95)
T 2lkz_A           84 GKTIGVDFAKS   94 (95)
T ss_dssp             TEEEEEEECCC
T ss_pred             CEEEEEEEccC
Confidence            99999999874

>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=99.85  E-value=1.4e-20  Score=130.39  Aligned_cols=86  Identities=24%  Similarity=0.501  Sum_probs=80.4

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +....+.++|||+|||..+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4455678999999999999999999999999999999999987 889999999999999999999999999999999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |++++++
T Consensus       100 V~~a~~k  106 (108)
T 2jrs_A          100 VGHVTER  106 (108)
T ss_dssp             EECSCSS
T ss_pred             EEEcccC
Confidence            9998764

>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=99.85  E-value=8.2e-21  Score=132.96  Aligned_cols=82  Identities=21%  Similarity=0.363  Sum_probs=74.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ..++|||+|||+++++++|+++|++||.|..|+|+.++. .++|||||+|.+.++|++||+.||+..|.|+.|+|.++.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            357899999999999999999999999999999998863 4789999999999999999999999999999999999876


Q ss_pred             CCC
Q 030010          102 NIA  104 (184)
Q Consensus       102 ~~~  104 (184)
                      ...
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=1.1e-20  Score=128.17  Aligned_cols=85  Identities=27%  Similarity=0.481  Sum_probs=78.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCC--C--CcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS--G--RSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~--~--~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.  +  ++++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            5689999999999999999999999999999999988763  3  78999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q 030010           97 EIVGTNIAT  105 (184)
Q Consensus        97 ~~~~~~~~~  105 (184)
                      +++.+....
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999875543

>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=99.84  E-value=1e-20  Score=131.15  Aligned_cols=88  Identities=24%  Similarity=0.406  Sum_probs=81.6

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||..||+..|.|+.|
T Consensus        19 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   98 (110)
T 1oo0_B           19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   98 (110)
T ss_dssp             CBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            34555678999999999999999999999999999999999987 88999999999999999999999999999999999


Q ss_pred             EEEEeeCCC
Q 030010           95 KIEIVGTNI  103 (184)
Q Consensus        95 ~V~~~~~~~  103 (184)
                      +|+++.+..
T Consensus        99 ~V~~a~~~~  107 (110)
T 1oo0_B           99 QVDWCFVKG  107 (110)
T ss_dssp             EEEESEESS
T ss_pred             EEEEcccCC
Confidence            999998654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.3e-20  Score=125.03  Aligned_cols=85  Identities=15%  Similarity=0.210  Sum_probs=79.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .+.....++|||+|||+.+++++|+++|++| .|..|.|+.+.+++++|||||+|.+.++|++||+ ||+..|.|+.|+|
T Consensus         4 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v   81 (91)
T 2dgw_A            4 GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEV   81 (91)
T ss_dssp             CCCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEE
T ss_pred             CCCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEE
Confidence            3455678999999999999999999999999 9999999999889999999999999999999999 9999999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      .++.+..
T Consensus        82 ~~a~~~~   88 (91)
T 2dgw_A           82 FREKSGP   88 (91)
T ss_dssp             EEESSCC
T ss_pred             EECCcCC
Confidence            9998653

>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=99.84  E-value=1.6e-20  Score=128.97  Aligned_cols=87  Identities=18%  Similarity=0.325  Sum_probs=79.7

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-C-CCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-S-GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~-~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .+.+..+.++|||+|||+.+++++|+++|++|| |..|.|+.++ + +++++||||+|.+.++|++|| .||+..|.++.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~   85 (104)
T 1wi8_A            8 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR   85 (104)
T ss_dssp             CCCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE
T ss_pred             CCCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcE
Confidence            345566789999999999999999999999999 9999999998 5 899999999999999999999 99999999999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      |+|+++.++..
T Consensus        86 l~V~~a~~~~~   96 (104)
T 1wi8_A           86 IRVDVADQAQD   96 (104)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEEccCCCC
Confidence            99999986443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.2e-20  Score=129.74  Aligned_cols=89  Identities=19%  Similarity=0.299  Sum_probs=82.1

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .......+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+. ++..|.|+.
T Consensus         8 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   86 (105)
T 2dh8_A            8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRN   86 (105)
T ss_dssp             CCCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEE
T ss_pred             CCcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEE
Confidence            345667788999999999999999999999999999999999997 889999999999999999999998 999999999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      |+|+++.++..
T Consensus        87 l~V~~a~~~~~   97 (105)
T 2dh8_A           87 IDPKPCTPRGM   97 (105)
T ss_dssp             EBCCCSCCSSC
T ss_pred             EEEEEccCCCC
Confidence            99999886554

>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=99.84  E-value=5.3e-20  Score=126.03  Aligned_cols=90  Identities=21%  Similarity=0.376  Sum_probs=81.4

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      +.......+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+  +++.|.|+
T Consensus         6 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~   83 (103)
T 2cqg_A            6 SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGR   83 (103)
T ss_dssp             SSCSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTE
T ss_pred             CCCCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCe
Confidence            3456667778999999999999999999999999999999999998 79999999999999999999998  57899999


Q ss_pred             eEEEEEeeCCCCC
Q 030010           93 PMKIEIVGTNIAT  105 (184)
Q Consensus        93 ~i~V~~~~~~~~~  105 (184)
                      .|.|+++.++...
T Consensus        84 ~l~v~~a~~~~~~   96 (103)
T 2cqg_A           84 WCDCKLPNSKQSQ   96 (103)
T ss_dssp             EEEEECCCTTCCC
T ss_pred             EEEEEecCCCCcC
Confidence            9999999876543

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

Probab=99.84  E-value=9.9e-21  Score=131.33  Aligned_cols=92  Identities=18%  Similarity=0.370  Sum_probs=80.0

Q ss_pred             CCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           10 PVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        10 ~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      ++..+.......+.++|||+|||..+++++|+++|++||.|..|.|+.++. .+++||||+|.+.++|++|++.||+..|
T Consensus        16 ~~~~S~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~   94 (109)
T 2err_A           16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVV   94 (109)
T ss_dssp             ------CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEE
T ss_pred             CCCCCCCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            444556677778899999999999999999999999999999999988764 4789999999999999999999999999


Q ss_pred             CCceEEEEEeeCC
Q 030010           90 DGKPMKIEIVGTN  102 (184)
Q Consensus        90 ~g~~i~V~~~~~~  102 (184)
                      .|+.|+|++++++
T Consensus        95 ~g~~l~V~~a~~~  107 (109)
T 2err_A           95 EGRKIEVNNATAR  107 (109)
T ss_dssp             TTEECEEEECCCS
T ss_pred             CCEEEEEEECCCC
Confidence            9999999998764

>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=99.84  E-value=8.9e-21  Score=128.71  Aligned_cols=85  Identities=21%  Similarity=0.267  Sum_probs=77.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .......++|||+|||+++++++|+++|++||.|..+.++.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   88 (98)
T 2cqp_A            9 SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (98)
T ss_dssp             CCCCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            3455667999999999999999999999999999888777776 889999999999999999999999999999999999


Q ss_pred             EEEeeC
Q 030010           96 IEIVGT  101 (184)
Q Consensus        96 V~~~~~  101 (184)
                      |+++..
T Consensus        89 V~~a~~   94 (98)
T 2cqp_A           89 LVLGSG   94 (98)
T ss_dssp             EEESSC
T ss_pred             EEEcCC
Confidence            999874

>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=99.83  E-value=7.2e-21  Score=132.75  Aligned_cols=84  Identities=24%  Similarity=0.358  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|| .||+..|.|+.|+|++
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            3456899999999999999999999999999999999998 7899999999999999999999 9999999999999999


Q ss_pred             eeCCCC
Q 030010           99 VGTNIA  104 (184)
Q Consensus        99 ~~~~~~  104 (184)
                      +.+...
T Consensus       101 a~~~~~  106 (114)
T 2cq4_A          101 SQAEKN  106 (114)
T ss_dssp             HHHHHH
T ss_pred             cCCCcc
Confidence            886543

>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=99.83  E-value=4.2e-20  Score=126.83  Aligned_cols=83  Identities=25%  Similarity=0.414  Sum_probs=76.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .......++|||+|||+.+++++|+++|++||.| .|.|+.+++++++|||||+|.+.++|++||+ +|+..|.++.|+|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (102)
T 1wez_A            9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            4556678999999999999999999999999955 9999999999999999999999999999994 7999999999999


Q ss_pred             EEeeC
Q 030010           97 EIVGT  101 (184)
Q Consensus        97 ~~~~~  101 (184)
                      .++.+
T Consensus        87 ~~~~~   91 (102)
T 1wez_A           87 FLNST   91 (102)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            98864

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.83  E-value=9.6e-21  Score=135.49  Aligned_cols=92  Identities=16%  Similarity=0.234  Sum_probs=83.4

Q ss_pred             CCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE--EEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCC-
Q 030010           12 QQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKR--YSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNV-   87 (184)
Q Consensus        12 ~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~--v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~-   87 (184)
                      .....+....+.++|||+|||+++++++|+++|++||.|..  |+|+.++ +++++|||||+|.+. +|++||+.||+. 
T Consensus        12 ~~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~   90 (131)
T 2m2b_A           12 SQGSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALH   90 (131)
T ss_dssp             CCCCCCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCC
Confidence            34445666678899999999999999999999999999976  9999999 999999999999999 999999999999 


Q ss_pred             ---ccCCceEEEEEeeCCCC
Q 030010           88 ---QLDGKPMKIEIVGTNIA  104 (184)
Q Consensus        88 ---~~~g~~i~V~~~~~~~~  104 (184)
                         .|.|+.|+|+++++...
T Consensus        91 ~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           91 PPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CSCCGGGCCCCCEECCCSCC
T ss_pred             CCccCCCEEEEEEECCCCCC
Confidence               99999999999987543

>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=99.83  E-value=4.5e-20  Score=122.56  Aligned_cols=82  Identities=22%  Similarity=0.476  Sum_probs=74.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +....+.++|||+|||+++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+ +++..|.|+.|.
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~   83 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVID   83 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEE
Confidence            4456678999999999999999999999999999999999998 89999999999999999999996 588899999999


Q ss_pred             EEEe
Q 030010           96 IEIV   99 (184)
Q Consensus        96 V~~~   99 (184)
                      |+++
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9875

>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=99.83  E-value=2.1e-20  Score=124.19  Aligned_cols=82  Identities=29%  Similarity=0.391  Sum_probs=75.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCC-cceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGR-SKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~-~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ..++|||+|||.++++++|+++|++||.|..|.|+.++ ++. +++||||+|.+.++|++|++.||+..|.|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            57899999999999999999999999999999998887 444 8999999999999999999999999999999999999


Q ss_pred             eCCC
Q 030010          100 GTNI  103 (184)
Q Consensus       100 ~~~~  103 (184)
                      .++.
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.83  E-value=3.4e-20  Score=123.51  Aligned_cols=79  Identities=27%  Similarity=0.535  Sum_probs=75.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|+ .||+..|.|+.|+|+++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            5799999999999999999999999999999999998 8999999999999999999999 9999999999999999876


Q ss_pred             C
Q 030010          102 N  102 (184)
Q Consensus       102 ~  102 (184)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.83  E-value=5.1e-21  Score=130.80  Aligned_cols=82  Identities=18%  Similarity=0.265  Sum_probs=77.3

Q ss_pred             CCCCEEEEcCCCC------CCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCC-c
Q 030010           21 ETGTKLYISNLDY------GVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG-K   92 (184)
Q Consensus        21 ~~~~~l~V~nLp~------~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g-~   92 (184)
                      ..+++|||+|||+      .+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999998 79999999999999999999999999999999 9


Q ss_pred             eEEEEEeeCC
Q 030010           93 PMKIEIVGTN  102 (184)
Q Consensus        93 ~i~V~~~~~~  102 (184)
                      .|+|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998753

>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=99.83  E-value=5.3e-21  Score=130.64  Aligned_cols=91  Identities=16%  Similarity=0.306  Sum_probs=73.8

Q ss_pred             CCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC--CCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030010           10 PVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR--SGRSKGTAEVVYSRRADAVAAVKRYNNV   87 (184)
Q Consensus        10 ~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~--~~~~~g~afV~F~~~e~a~~Ai~~l~g~   87 (184)
                      ++.....+......++|||+|||+++++++|+++|++|| |..|.|+.++  +++++|||||+|.+.++|++|| .||+.
T Consensus         6 ~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~   83 (100)
T 2j76_E            6 HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   83 (100)
T ss_dssp             --------------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTC
T ss_pred             CCCCCCCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCC
Confidence            333444556677789999999999999999999999999 9999999886  7899999999999999999999 89999


Q ss_pred             ccCCceEEEEEeeCC
Q 030010           88 QLDGKPMKIEIVGTN  102 (184)
Q Consensus        88 ~~~g~~i~V~~~~~~  102 (184)
                      .|.|+.|+|+++++.
T Consensus        84 ~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           84 SLGNRRIRVDVADQA   98 (100)
T ss_dssp             CBTTBCCCCEECCCS
T ss_pred             EECCeEEEEEeccCC
Confidence            999999999998764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=4.2e-20  Score=126.09  Aligned_cols=86  Identities=24%  Similarity=0.470  Sum_probs=77.0

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      +.+....+.++|||+|||+.+++++|+++|++||.|   .|+.+.++++++||||+|.+.++|++||+.||+..|.++.|
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   83 (101)
T 2fc9_A            7 GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAI   83 (101)
T ss_dssp             CCCCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEE
T ss_pred             CCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            344566678999999999999999999999999976   56666788899999999999999999999999999999999


Q ss_pred             EEEEeeCCC
Q 030010           95 KIEIVGTNI  103 (184)
Q Consensus        95 ~V~~~~~~~  103 (184)
                      +|+++.++.
T Consensus        84 ~v~~a~~~~   92 (101)
T 2fc9_A           84 RLELQGPRG   92 (101)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEcCCCC
Confidence            999998653

>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=99.83  E-value=1.4e-19  Score=126.17  Aligned_cols=86  Identities=21%  Similarity=0.360  Sum_probs=79.1

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc------
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL------   89 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~------   89 (184)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|      
T Consensus        18 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             hcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccc
Confidence            34555678999999999999999999999999999999999999889999999999999999999999999999      


Q ss_pred             --CCceEEEEEeeC
Q 030010           90 --DGKPMKIEIVGT  101 (184)
Q Consensus        90 --~g~~i~V~~~~~  101 (184)
                        .+++|.|.++.+
T Consensus        98 ~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           98 SAPTEPLLCKFSGP  111 (114)
T ss_dssp             CCCSSCBEEEECCC
T ss_pred             cCCCCceeEEccCC
Confidence              578899999874

>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=99.83  E-value=4.6e-20  Score=136.87  Aligned_cols=89  Identities=24%  Similarity=0.402  Sum_probs=80.8

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+....++++|||+|||+.+++++|+.+|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus        65 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  144 (165)
T 1rk8_A           65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI  144 (165)
T ss_dssp             -CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34456678899999999999999999999999999999999997 89999999999999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      .|.++.+...
T Consensus       145 ~V~~a~~~~~  154 (165)
T 1rk8_A          145 QVDWCFVKGP  154 (165)
T ss_dssp             EEEESEECC-
T ss_pred             EEEEecCCCC
Confidence            9999987554

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

Probab=99.83  E-value=5.4e-20  Score=132.35  Aligned_cols=86  Identities=24%  Similarity=0.423  Sum_probs=79.1

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      +.......+.++|||+|||..+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+
T Consensus        54 ~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  133 (140)
T 2ku7_A           54 GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR  133 (140)
T ss_dssp             CSSCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTE
T ss_pred             CCCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3345666778999999999999999999999999999999999997 889999999999999999999999999999999


Q ss_pred             eEEEEEe
Q 030010           93 PMKIEIV   99 (184)
Q Consensus        93 ~i~V~~~   99 (184)
                      .|+|+++
T Consensus       134 ~l~v~~A  140 (140)
T 2ku7_A          134 TIRVNLA  140 (140)
T ss_dssp             EEEEEC-
T ss_pred             EEEEEeC
Confidence            9999875

>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=99.83  E-value=8e-20  Score=125.64  Aligned_cols=86  Identities=21%  Similarity=0.295  Sum_probs=78.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .+.....++|||+|||+.+++++|+++|++||.|.. |.|+.+.+++++|||||+|.+.++|++||+. |+..|.++.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~   87 (104)
T 1wg5_A            9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE   87 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEE
Confidence            344567899999999999999999999999999987 8888888899999999999999999999987 99999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |.++....
T Consensus        88 v~~~~~~~   95 (104)
T 1wg5_A           88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            99987543

>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=99.83  E-value=8e-20  Score=134.26  Aligned_cols=89  Identities=25%  Similarity=0.405  Sum_probs=81.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .......++|||+|||+++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        64 ~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  143 (158)
T 2kn4_A           64 HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  143 (158)
T ss_dssp             CCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3444568999999999999999999999999999999999997 899999999999999999999999999999999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |.++.+..+.
T Consensus       144 v~~a~~~~~~  153 (158)
T 2kn4_A          144 VQMARYGRPP  153 (158)
T ss_dssp             EEEECCSSCC
T ss_pred             EEECCCCCCC
Confidence            9999875543

>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=99.83  E-value=9.9e-21  Score=127.70  Aligned_cols=84  Identities=21%  Similarity=0.263  Sum_probs=74.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v   89 (95)
T 2ek1_A           10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (95)
T ss_dssp             -----CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            334456999999999999999999999999999888888777 8899999999999999999999999999999999999


Q ss_pred             EEeeC
Q 030010           97 EIVGT  101 (184)
Q Consensus        97 ~~~~~  101 (184)
                      +++..
T Consensus        90 ~~a~s   94 (95)
T 2ek1_A           90 SGPSS   94 (95)
T ss_dssp             ECCC-
T ss_pred             EeccC
Confidence            98753

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=9.4e-20  Score=122.36  Aligned_cols=82  Identities=27%  Similarity=0.420  Sum_probs=74.7

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .+....+.++|||+|||+.+++++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus         3 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   75 (92)
T 2dgt_A            3 SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMH   75 (92)
T ss_dssp             CSCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            45566778999999999999999999999999999999987       34999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q 030010           96 IEIVGTNIA  104 (184)
Q Consensus        96 V~~~~~~~~  104 (184)
                      |++++++..
T Consensus        76 V~~a~~~~~   84 (92)
T 2dgt_A           76 VQLSTSRLR   84 (92)
T ss_dssp             EEESSCCCS
T ss_pred             EEEccCCCC
Confidence            999986544

>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=99.82  E-value=7e-21  Score=133.07  Aligned_cols=86  Identities=15%  Similarity=0.249  Sum_probs=79.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCe-EEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDL-KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i-~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .....+.++|||+|||+.+++++|+++|++||.| ..|.|+.+++++++|||||+|.+.++|++||+. |+..|.++.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~   87 (114)
T 2cpy_A            9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAF   87 (114)
T ss_dssp             CSCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEE
T ss_pred             CCCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEE
Confidence            3445668999999999999999999999999999 889999999999999999999999999999986 99999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |.++.+..
T Consensus        88 v~~a~~~~   95 (114)
T 2cpy_A           88 VHVVTLED   95 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99998654

>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=99.82  E-value=1.2e-20  Score=129.26  Aligned_cols=87  Identities=23%  Similarity=0.544  Sum_probs=80.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         3 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   82 (104)
T 1p1t_A            3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRV   82 (104)
T ss_dssp             CSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEE
T ss_pred             CcCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            334457899999999999999999999999999999999997 8899999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      +++.+...
T Consensus        83 ~~a~~~~~   90 (104)
T 1p1t_A           83 DNAASEKN   90 (104)
T ss_dssp             EETTCTTH
T ss_pred             EeCCCccc
Confidence            99986544

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

Probab=99.82  E-value=1.5e-19  Score=120.90  Aligned_cols=80  Identities=23%  Similarity=0.336  Sum_probs=73.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      +...+.++|||+|||+++++++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|.++.|+|+
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             SCSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            345678999999999999999999999999999999997       5799999999999999999999999999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ++++...
T Consensus        76 ~a~~~~~   82 (90)
T 2dnq_A           76 ASKNKSK   82 (90)
T ss_dssp             CSSCCCC
T ss_pred             ECCCCCC
Confidence            9986544

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

Probab=99.82  E-value=3.8e-20  Score=127.30  Aligned_cols=81  Identities=17%  Similarity=0.193  Sum_probs=76.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ....++|||+|||+.+|+++|+++|++||.|..|.|+.++.++++|||||+|.+.++|++||. +++..|.|+.|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999999999888899999999999999999998 8999999999999987


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

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

Probab=99.82  E-value=4e-20  Score=127.35  Aligned_cols=83  Identities=17%  Similarity=0.193  Sum_probs=73.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCceEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN--VQLDGKPMK   95 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g--~~~~g~~i~   95 (184)
                      ....+.++|||+|||+.++|++|+++|++||.|..|.|+.+     +|||||+|.+.++|++||+.|++  ..|.|++|+
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            34556899999999999999999999999999999999865     68999999999999999998864  789999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |++++++...
T Consensus        86 V~~A~~~~~~   95 (105)
T 1sjq_A           86 IQFSNHKELK   95 (105)
T ss_dssp             BCCCSSSSCC
T ss_pred             EEEcCCCCCC
Confidence            9999865443

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.82  E-value=5.6e-20  Score=129.34  Aligned_cols=86  Identities=19%  Similarity=0.235  Sum_probs=79.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCC---eEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGD---LKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~---i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .......++|||+|||+++++++|+++|+.||.   |..|+|+.++.++++|||||+|.+.++|++||+ +|+..|.++.
T Consensus        11 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~   89 (118)
T 2db1_A           11 GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRY   89 (118)
T ss_dssp             SSCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeE
Confidence            344567899999999999999999999999999   899999999889999999999999999999998 9999999999


Q ss_pred             EEEEEeeCCC
Q 030010           94 MKIEIVGTNI  103 (184)
Q Consensus        94 i~V~~~~~~~  103 (184)
                      |+|.++....
T Consensus        90 i~V~~a~~~~   99 (118)
T 2db1_A           90 IEVFKSHRTE   99 (118)
T ss_dssp             EEEEEECHHH
T ss_pred             EEEEECCHHH
Confidence            9999987543

>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=99.82  E-value=5.7e-21  Score=138.23  Aligned_cols=83  Identities=24%  Similarity=0.388  Sum_probs=73.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      +......++|||+|||+++||++|+++|++|| |..|.|+.+++++++|||||+|.+.++|++|| .+|+..|.++.|+|
T Consensus        40 ~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V  117 (139)
T 2hgn_A           40 TVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIEL  117 (139)
T ss_dssp             -----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEE
Confidence            34556778999999999999999999999999 66999999988999999999999999999999 78999999999999


Q ss_pred             EEeeC
Q 030010           97 EIVGT  101 (184)
Q Consensus        97 ~~~~~  101 (184)
                      .++..
T Consensus       118 ~~a~~  122 (139)
T 2hgn_A          118 FLNST  122 (139)
T ss_dssp             EECCC
T ss_pred             EECCC
Confidence            98865

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

Probab=99.82  E-value=1.8e-20  Score=134.90  Aligned_cols=90  Identities=24%  Similarity=0.408  Sum_probs=82.6

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .++...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|
T Consensus        40 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            35556678899999999999999999999999999999999988 88999999999999999999999999999999999


Q ss_pred             EEEEeeCCCCC
Q 030010           95 KIEIVGTNIAT  105 (184)
Q Consensus        95 ~V~~~~~~~~~  105 (184)
                      +|+++++...+
T Consensus       120 ~V~~a~~~~~~  130 (135)
T 2lea_A          120 RVQMARYGRPP  130 (135)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99999875543

>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=99.81  E-value=2.2e-19  Score=124.09  Aligned_cols=86  Identities=19%  Similarity=0.246  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCC-eEEEEEE-eCC-CCCcceEEEEEecCHHHHHHHHHHhC--CCccCCceE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGD-LKRYSIH-YDR-SGRSKGTAEVVYSRRADAVAAVKRYN--NVQLDGKPM   94 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~-i~~v~i~-~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~--g~~~~g~~i   94 (184)
                      ..+.++|||+|||+.+++++|+++|++||. |..|.|+ .++ ++++++||||+|.+.++|++||+.|+  +..|.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            345799999999999999999999999998 9999988 666 78899999999999999999999996  589999999


Q ss_pred             EEEEeeCCCCC
Q 030010           95 KIEIVGTNIAT  105 (184)
Q Consensus        95 ~V~~~~~~~~~  105 (184)
                      +|+++.+....
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999876553

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=7.5e-20  Score=126.90  Aligned_cols=86  Identities=21%  Similarity=0.376  Sum_probs=74.5

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.+ +..|.|+.|+
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~   97 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTID   97 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEE
Confidence            3455668999999999999999999999999999999999998 7999999999999999999999876 4999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |+++.+..
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99998644

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.3e-20  Score=124.70  Aligned_cols=80  Identities=20%  Similarity=0.266  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            4568999999999999999999999999999999999997 889999999999999999999999999999999887665


Q ss_pred             e
Q 030010           99 V   99 (184)
Q Consensus        99 ~   99 (184)
                      .
T Consensus        82 ~   82 (85)
T 1x4e_A           82 P   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.81  E-value=1.3e-19  Score=128.05  Aligned_cols=81  Identities=31%  Similarity=0.564  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|| .||+..|.|+.|+|++++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            35899999999999999999999999999999999997 8999999999999999999999 799999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

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

Probab=99.81  E-value=1.4e-19  Score=123.45  Aligned_cols=81  Identities=21%  Similarity=0.232  Sum_probs=72.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc--cCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQ--LDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~--~~g~~i   94 (184)
                      .....++++|||+|||+.+++++|+++|++||.|..|.++.     .++||||+|.+.++|++||+.|++..  |.|++|
T Consensus        15 ~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             --CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             cccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            34556789999999999999999999999999999999874     36799999999999999999999865  789999


Q ss_pred             EEEEeeCC
Q 030010           95 KIEIVGTN  102 (184)
Q Consensus        95 ~V~~~~~~  102 (184)
                      .|++++.+
T Consensus        90 ~V~~S~~k   97 (100)
T 3r27_A           90 FVNYSTSQ   97 (100)
T ss_dssp             EEEECSCS
T ss_pred             EEEecccc
Confidence            99999764

>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=99.81  E-value=7.1e-20  Score=128.19  Aligned_cols=80  Identities=23%  Similarity=0.375  Sum_probs=65.2

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce-
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP-   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~-   93 (184)
                      ..+++....++|||+|||+++++++|+++|++||.|..|.|+.+      +||||+|.+.++|++||+.||+.+|.|+. 
T Consensus         8 ~gpp~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~   81 (115)
T 3beg_B            8 YGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   81 (115)
T ss_dssp             ---------CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTS
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEe
Confidence            34455567899999999999999999999999999999999754      79999999999999999999999999998 


Q ss_pred             ----EEEEEee
Q 030010           94 ----MKIEIVG  100 (184)
Q Consensus        94 ----i~V~~~~  100 (184)
                          |+|....
T Consensus        82 ~~~~i~v~~~~   92 (115)
T 3beg_B           82 ETAYIRVKVDG   92 (115)
T ss_dssp             CCCBCEEEECC
T ss_pred             eeEEEEeccCC
Confidence                5555544

>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=99.81  E-value=3.4e-19  Score=122.77  Aligned_cols=84  Identities=14%  Similarity=0.109  Sum_probs=74.0

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCce
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN--VQLDGKP   93 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g--~~~~g~~   93 (184)
                      .+....++++|||+|||+.+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.|++  ..|.|++
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~   82 (104)
T 1wex_A            8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            3455667899999999999999999999999999999998753     67999999999999999998865  4699999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      |+|++++.+..
T Consensus        83 l~V~~a~~~~~   93 (104)
T 1wex_A           83 AFFNYSTSKRI   93 (104)
T ss_dssp             CEEEECSSSSC
T ss_pred             EEEEEccCccc
Confidence            99999986543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.8e-19  Score=122.13  Aligned_cols=84  Identities=25%  Similarity=0.357  Sum_probs=75.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .....+.++|||+|||+++++++|+++|+.|.   .|.++.++ ++++++||||+|.+.++|++||+.||+..|.++.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            45566789999999999999999999999873   57788887 889999999999999999999999999999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |++++++.
T Consensus        86 V~~a~~~~   93 (102)
T 2fc8_A           86 LDWAKPKG   93 (102)
T ss_dssp             EEECCCCC
T ss_pred             EEEecCCC
Confidence            99998643

>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=99.81  E-value=3.7e-20  Score=131.16  Aligned_cols=86  Identities=17%  Similarity=0.304  Sum_probs=76.4

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEE-eCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIH-YDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~-~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ..+....++|||+|||+.+++++|+++|++||.|..+.++ .+.+++++|||||+|.+.++|++||+ ||+..|.|+.|.
T Consensus        19 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   97 (124)
T 1wel_A           19 RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   97 (124)
T ss_dssp             SSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            4556678999999999999999999999999999874444 44589999999999999999999999 999999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |.++..+.
T Consensus        98 V~~a~~~~  105 (124)
T 1wel_A           98 VHPITKKG  105 (124)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99987643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.81  E-value=1.1e-19  Score=120.62  Aligned_cols=74  Identities=22%  Similarity=0.263  Sum_probs=70.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .+..|||+||++.+||++|+++|.+||+|..++++.     ++|||||+|.+.++|++||+.||+..+.+++|+|+++.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            478999999999999999999999999999999975     58999999999999999999999999999999999985

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

Probab=99.81  E-value=7.9e-20  Score=127.83  Aligned_cols=84  Identities=24%  Similarity=0.348  Sum_probs=77.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+. ++..|.|+.|+|++
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            4456999999999999999999999999999999999997 789999999999999999999987 99999999999999


Q ss_pred             eeCCCC
Q 030010           99 VGTNIA  104 (184)
Q Consensus        99 ~~~~~~  104 (184)
                      +.++..
T Consensus       103 a~~~~~  108 (116)
T 1x4b_A          103 AVAREE  108 (116)
T ss_dssp             CSSCCC
T ss_pred             CCCCcc
Confidence            886543

>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=99.81  E-value=9.4e-20  Score=126.71  Aligned_cols=87  Identities=22%  Similarity=0.394  Sum_probs=78.4

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHH---HHHhhCCCeEEEEEEeCC-CC---CcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIK---ELFSEVGDLKRYSIHYDR-SG---RSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~---~~f~~~G~i~~v~i~~~~-~~---~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      .......++|||+|||+.+++++|+   ++|++||.|..|.|+.++ ++   +++|||||+|.+.++|++||+.||+..|
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            3445568899999999999999999   999999999999998887 33   5669999999999999999999999999


Q ss_pred             CCceEEEEEeeCCC
Q 030010           90 DGKPMKIEIVGTNI  103 (184)
Q Consensus        90 ~g~~i~V~~~~~~~  103 (184)
                      .|+.|+|+++.++.
T Consensus        89 ~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           89 DGRTLKASLGTTKY  102 (111)
T ss_dssp             TTEEEEEESCCCCS
T ss_pred             CCEEEEEEeccccc
Confidence            99999999998654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=2.6e-19  Score=127.60  Aligned_cols=85  Identities=24%  Similarity=0.379  Sum_probs=75.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHH----HHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIK----ELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~----~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      +....++++|||+|||+.+++++|+    ++|++||.|..|.+.  ++++++|||||+|.+.++|++||+.||+..|.|+
T Consensus        23 ~~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr  100 (127)
T 2a3j_A           23 PPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN  100 (127)
T ss_dssp             CCCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            4556678999999999999999876    699999999888764  4678899999999999999999999999999999


Q ss_pred             eEEEEEeeCCC
Q 030010           93 PMKIEIVGTNI  103 (184)
Q Consensus        93 ~i~V~~~~~~~  103 (184)
                      +|+|.+++...
T Consensus       101 ~l~V~~a~~~~  111 (127)
T 2a3j_A          101 PLVITFSETPQ  111 (127)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEEccCcc
Confidence            99999998654

>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=99.81  E-value=1.1e-19  Score=124.74  Aligned_cols=82  Identities=20%  Similarity=0.214  Sum_probs=73.1

Q ss_pred             CCCCCCCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCceE
Q 030010           18 SAIETGTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN--VQLDGKPM   94 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g--~~~~g~~i   94 (184)
                      ...+++++|||+|||+ .+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.||+  ..|.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           10 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            3455789999999999 9999999999999999999999865     46999999999999999999886  45999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      +|++++....
T Consensus        85 ~V~~a~~~~~   94 (102)
T 1x4d_A           85 RVHLSQKYKR   94 (102)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEECCCCCC
Confidence            9999986543

>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=99.81  E-value=8.5e-20  Score=131.59  Aligned_cols=85  Identities=19%  Similarity=0.240  Sum_probs=78.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCC---eEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGD---LKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~---i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .+.....++|||+|||+++|+++|+++|++||.   |..|.|+.++.++++|||||+|.+.++|++||+ ||+..|.++.
T Consensus        38 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           38 GPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             CSSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            345567899999999999999999999999999   889999999889999999999999999999998 9999999999


Q ss_pred             EEEEEeeCC
Q 030010           94 MKIEIVGTN  102 (184)
Q Consensus        94 i~V~~~~~~  102 (184)
                      |+|.++...
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999998653

>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=99.81  E-value=2.9e-19  Score=121.10  Aligned_cols=81  Identities=15%  Similarity=0.251  Sum_probs=73.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC--CceEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD--GKPMK   95 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~--g~~i~   95 (184)
                      ....+.++|||+|||+++++++|+++|++||.|..|.|..+     ++||||+|.+.++|++||+.||+..|.  ++.|+
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            34456799999999999999999999999999999988754     679999999999999999999999999  99999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |++++++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998643

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

Probab=99.80  E-value=1.7e-19  Score=135.51  Aligned_cols=89  Identities=55%  Similarity=0.939  Sum_probs=82.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      +....++++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        82 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V  161 (177)
T 2f3j_A           82 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  161 (177)
T ss_dssp             CSSCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q 030010           97 EIVGTNIAT  105 (184)
Q Consensus        97 ~~~~~~~~~  105 (184)
                      +++......
T Consensus       162 ~~a~~~~~~  170 (177)
T 2f3j_A          162 QLVASQIDL  170 (177)
T ss_dssp             EEESSGGGG
T ss_pred             EEecCCCCC
Confidence            999875543

>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=99.80  E-value=4.2e-19  Score=121.66  Aligned_cols=83  Identities=17%  Similarity=0.169  Sum_probs=73.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN--NVQLDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~--g~~~~g~~i   94 (184)
                      .....++++|||+|||+.+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.|+  +..|.|++|
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            445567899999999999999999999999999999988754     6899999999999999999774  678999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      +|.+++....
T Consensus        84 ~V~~a~~~~~   93 (101)
T 2cq1_A           84 YIQYSNHKEL   93 (101)
T ss_dssp             EEEECSCSSC
T ss_pred             EEEEcCcccC
Confidence            9999986544

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=7.1e-19  Score=119.60  Aligned_cols=82  Identities=30%  Similarity=0.452  Sum_probs=74.2

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhC--CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEV--GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~--G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      .......+.++|||+|||+.+++++|+++|++|  |.|..|.+.       ++||||+|.+.++|++||+.||+..|.|+
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (99)
T 2cpd_A            7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGS   79 (99)
T ss_dssp             CCCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTE
T ss_pred             ccccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            345566778999999999999999999999999  999998875       56999999999999999999999999999


Q ss_pred             eEEEEEeeCCC
Q 030010           93 PMKIEIVGTNI  103 (184)
Q Consensus        93 ~i~V~~~~~~~  103 (184)
                      .|+|+++++..
T Consensus        80 ~l~v~~a~~~~   90 (99)
T 2cpd_A           80 PIEVTLAKPVD   90 (99)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998644

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

Probab=99.80  E-value=5.6e-20  Score=118.78  Aligned_cols=74  Identities=16%  Similarity=0.361  Sum_probs=70.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +|||+|||+++++++|+++|++||.|..|.++.++ +++++|||||+|.+.++|++|++ +|+..|.|+.|+|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999998 89999999999999999999997 9999999999999874

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=9e-20  Score=126.69  Aligned_cols=82  Identities=12%  Similarity=0.271  Sum_probs=75.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      +.....++|||+|||+.+++++|+++|++| .|..|.|+.++.++++|||||+|.+.++|++|| .+|+..|.++.|.|.
T Consensus        11 ~~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~   88 (109)
T 2dnn_A           11 PINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVS   88 (109)
T ss_dssp             CCCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEE
Confidence            334456899999999999999999999999 899999999988999999999999999999999 689999999999998


Q ss_pred             EeeC
Q 030010           98 IVGT  101 (184)
Q Consensus        98 ~~~~  101 (184)
                      .+..
T Consensus        89 ~a~~   92 (109)
T 2dnn_A           89 PATE   92 (109)
T ss_dssp             ECCH
T ss_pred             ECCc
Confidence            8764

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

Probab=99.80  E-value=3.2e-19  Score=121.21  Aligned_cols=85  Identities=20%  Similarity=0.293  Sum_probs=71.3

Q ss_pred             CCCCCCCCCCCCCCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           11 VQQAGRASAIETGTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        11 ~~~~~~~~~~~~~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      +..........++++|||+|||+ ++++++|+++|++||.|..|.|.       ++||||+|.+.++|++||+.||+..|
T Consensus        10 ~~~~~~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (97)
T 2xnq_A           10 HSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMN   82 (97)
T ss_dssp             ---------CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEE
T ss_pred             CCcccccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            33344455566789999999998 99999999999999999999884       78999999999999999999999999


Q ss_pred             CCceEEEEEeeCC
Q 030010           90 DGKPMKIEIVGTN  102 (184)
Q Consensus        90 ~g~~i~V~~~~~~  102 (184)
                      .|+.|+|++++..
T Consensus        83 ~g~~l~V~~a~~~   95 (97)
T 2xnq_A           83 FGKKLILEVSSSN   95 (97)
T ss_dssp             TTEECEEEECCCC
T ss_pred             CCEEEEEEecCCC
Confidence            9999999998753

>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=99.80  E-value=2.6e-20  Score=124.46  Aligned_cols=82  Identities=24%  Similarity=0.491  Sum_probs=72.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      ++|||+|||.++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.+ |++|++.||+..|.|+.|+|+++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            589999999999999999999999999999999998 7899999999999999 99999999999999999999999876


Q ss_pred             CCCC
Q 030010          103 IATR  106 (184)
Q Consensus       103 ~~~~  106 (184)
                      ....
T Consensus        81 ~~~~   84 (90)
T 2ki2_A           81 KSLE   84 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            5543

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

Probab=99.80  E-value=3.1e-19  Score=119.36  Aligned_cols=79  Identities=22%  Similarity=0.378  Sum_probs=72.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus         4 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             CSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345678999999999999999999999999999999997       3499999999999999999999999999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      ++++..
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            998653

>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=99.80  E-value=6.4e-20  Score=127.97  Aligned_cols=86  Identities=26%  Similarity=0.375  Sum_probs=75.5

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE----EEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLK----RYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~----~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      .....+.++|||+|||+.+++++|+++|++||.|.    .+.+.   ++++++||||+|.+.++|++||+.||+..|.|+
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   95 (115)
T 2cpx_A           19 YNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGK   95 (115)
T ss_dssp             CCCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSC
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            34456789999999999999999999999999984    44444   778899999999999999999999999999999


Q ss_pred             eEEEEEeeCCCCC
Q 030010           93 PMKIEIVGTNIAT  105 (184)
Q Consensus        93 ~i~V~~~~~~~~~  105 (184)
                      .|+|+++.+....
T Consensus        96 ~l~v~~a~~~~~~  108 (115)
T 2cpx_A           96 ILVIEFGKNKKQR  108 (115)
T ss_dssp             BCEEEECCCCSCC
T ss_pred             EEEEEEccCCCCC
Confidence            9999999875543

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

Probab=99.80  E-value=6e-20  Score=119.06  Aligned_cols=75  Identities=23%  Similarity=0.445  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ++|||+|||+++++++|+++|++||.|..|.++.++ +++++|||||+|.+.++|++|++.++ ..|.|+.|+|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            579999999999999999999999999999999998 78999999999999999999999999 9999999999986

>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=99.80  E-value=3.4e-19  Score=117.69  Aligned_cols=81  Identities=19%  Similarity=0.379  Sum_probs=73.9

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCce
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY-NNVQLDGKP   93 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l-~g~~~~g~~   93 (184)
                      ..++...+.++|||+|||..+++++|+++|++||.|..|.++.+     ++||||+|.+.++|++|++.| ++..|.|+.
T Consensus         4 ~~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CCCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            34556677899999999999999999999999999999999853     689999999999999999988 999999999


Q ss_pred             EEEEEee
Q 030010           94 MKIEIVG  100 (184)
Q Consensus        94 i~V~~~~  100 (184)
                      |+|++++
T Consensus        79 l~v~~ak   85 (85)
T 2ytc_A           79 LNVKWGR   85 (85)
T ss_dssp             CCEEECC
T ss_pred             EEEEecC
Confidence            9999874

>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=99.80  E-value=3.4e-19  Score=125.42  Aligned_cols=83  Identities=19%  Similarity=0.205  Sum_probs=74.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCceEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN--VQLDGKPMK   95 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g--~~~~g~~i~   95 (184)
                      ....++++|||+|||+.+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.|++  ..|.|++|+
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            34556899999999999999999999999999999999865     68999999999999999998874  789999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |++++.....
T Consensus       101 V~~a~~k~~~  110 (119)
T 2ad9_A          101 IQFSNHKELK  110 (119)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCCCCC
Confidence            9999865543

>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=99.80  E-value=5.3e-19  Score=122.35  Aligned_cols=82  Identities=17%  Similarity=0.287  Sum_probs=75.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...+.++|||+|||..+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            4456899999999999999999999999999999999865     67999999999999999999999999999999999


Q ss_pred             eeCCCCC
Q 030010           99 VGTNIAT  105 (184)
Q Consensus        99 ~~~~~~~  105 (184)
                      +++....
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            9875543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.80  E-value=2.5e-19  Score=123.38  Aligned_cols=83  Identities=22%  Similarity=0.313  Sum_probs=75.5

Q ss_pred             CCCCCCEEEEcCCCCCC------CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           19 AIETGTKLYISNLDYGV------SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~------te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      .....++|||+|||+.+      ++++|+++|++||.|..|.|+ ..+++++|||||+|.+.++|++||+.||+..|.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34457899999999999      789999999999999999887 34889999999999999999999999999999998


Q ss_pred             -eEEEEEeeCC
Q 030010           93 -PMKIEIVGTN  102 (184)
Q Consensus        93 -~i~V~~~~~~  102 (184)
                       .|+|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998754

>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=99.80  E-value=8e-19  Score=119.34  Aligned_cols=83  Identities=23%  Similarity=0.404  Sum_probs=75.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .....+.++|||+|||+.+++++|+++|++||.|..|.|..+     ++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A            9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            345567899999999999999999999999999999999844     679999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      +++++...
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpj_A           84 RFACHSAS   91 (99)
T ss_dssp             EESSCCSC
T ss_pred             EEcCCCCC
Confidence            99987543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.79  E-value=1.4e-19  Score=126.05  Aligned_cols=80  Identities=23%  Similarity=0.307  Sum_probs=72.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCC-CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVG-DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G-~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ....++|||+|||+.+++++|+++|++|| .|..+.|...   +++|||||+|.+.++|++||+.||+.+|.|+.|+|++
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34578999999999999999999999999 8999888532   4689999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8753

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

Probab=99.79  E-value=3e-19  Score=123.76  Aligned_cols=81  Identities=19%  Similarity=0.358  Sum_probs=72.6

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .+....+.++|||+|||+++++++|+++|++||.|..|.|+       ++||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        24 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             ----CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            34556778999999999999999999999999999999987       67999999999999999999999999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |+++++..
T Consensus        97 V~~a~~~~  104 (108)
T 2jvo_A           97 VVYSKLPA  104 (108)
T ss_dssp             EESCSCCC
T ss_pred             EEEecCCC
Confidence            99998644

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=6.4e-19  Score=119.46  Aligned_cols=81  Identities=17%  Similarity=0.326  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .....++|||+|||+++++++|+++|++||.|. +.++.+   ++++||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            445578999999999999999999999999996 666643   5688999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      ++++.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98643

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

Probab=99.79  E-value=4.1e-19  Score=120.24  Aligned_cols=80  Identities=23%  Similarity=0.347  Sum_probs=71.5

Q ss_pred             CCCCCCCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||+ .+++++|+++|++||.|..|.|.       ++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ----CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             ccCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            3456789999999999 99999999999999999999985       679999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      +++++...
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99986544

>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=99.79  E-value=7.4e-20  Score=126.45  Aligned_cols=86  Identities=13%  Similarity=0.227  Sum_probs=78.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCC---eEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGD---LKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~---i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .......++|||+|||+++++++|+++|+.||.   |..|.|+.++.++++|||||+|.+.++|++||+ +|+..|.++.
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~   83 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRY   83 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSC
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeE
Confidence            345567899999999999999999999999988   899999998889999999999999999999998 9999999999


Q ss_pred             EEEEEeeCCC
Q 030010           94 MKIEIVGTNI  103 (184)
Q Consensus        94 i~V~~~~~~~  103 (184)
                      |+|.++.+..
T Consensus        84 i~V~~a~~~~   93 (107)
T 2lmi_A           84 VEVYEINNED   93 (107)
T ss_dssp             CCCEECCHHH
T ss_pred             EEEEECCHHH
Confidence            9999987643

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

Probab=99.79  E-value=5.1e-19  Score=120.68  Aligned_cols=76  Identities=25%  Similarity=0.363  Sum_probs=71.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNI  103 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~  103 (184)
                      ++|||+|||+++++++|+++|++||.|..|.|+.+    +++||||+|.+.++|++|++.||+..|.|+.|+|+++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            58999999999999999999999999999999876    67899999999999999999999999999999999998754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.79  E-value=4.9e-20  Score=125.74  Aligned_cols=84  Identities=21%  Similarity=0.205  Sum_probs=74.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||+++++++|+++|++||.|.. .++.++ ++++++||||+|.+.++|++||+ ||+..|.|+.|+|
T Consensus        12 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V   89 (101)
T 1fj7_A           12 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   89 (101)
T ss_dssp             TTCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEE
Confidence            34456889999999999999999999999999877 455555 78899999999999999999998 9999999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      +++.+..
T Consensus        90 ~~a~~~~   96 (101)
T 1fj7_A           90 EKPKGRD   96 (101)
T ss_dssp             ECCSCCC
T ss_pred             EEcCCCC
Confidence            9987643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.79  E-value=8.2e-19  Score=134.94  Aligned_cols=85  Identities=27%  Similarity=0.335  Sum_probs=76.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .+..+.++|||+|||++++|++|+++|++||+|..|+|+.++ +++++|||||+|.+.++|++||+.+|+..+.++.|+|
T Consensus        10 ~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~   89 (213)
T 4f02_A           10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI   89 (213)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccc
Confidence            345567899999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEeeCC
Q 030010           97 EIVGTN  102 (184)
Q Consensus        97 ~~~~~~  102 (184)
                      .++...
T Consensus        90 ~~~~~~   95 (213)
T 4f02_A           90 MWSQRD   95 (213)
T ss_dssp             EECCCC
T ss_pred             cccccc
Confidence            987653

>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=99.79  E-value=1.7e-19  Score=122.01  Aligned_cols=84  Identities=24%  Similarity=0.457  Sum_probs=74.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHH----HHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIK----ELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~----~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      +...++++|||+|||+.+++++|+    ++|++||.|..|.|.  +++++++||||+|.+.++|++|++.||+..|.|+.
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~--~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECC--HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEE--cCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            345678999999999999999999    999999999998876  35567899999999999999999999999999999


Q ss_pred             EEEEEeeCCC
Q 030010           94 MKIEIVGTNI  103 (184)
Q Consensus        94 i~V~~~~~~~  103 (184)
                      |+|+++++..
T Consensus        81 l~v~~a~~~~   90 (97)
T 1nu4_A           81 MRIQYAKTDS   90 (97)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEccCCC
Confidence            9999998754

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.6e-19  Score=119.11  Aligned_cols=79  Identities=28%  Similarity=0.384  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCC-eEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccCCceEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGD-LKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN-VQLDGKPMKI   96 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~-i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g-~~~~g~~i~V   96 (184)
                      ...+.++|||+|||+++++++|+++|++||. |..+.+.      +++||||+|.+.++|++||+.||+ ..|.|+.|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            4456799999999999999999999999999 6655553      478999999999999999999999 9999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      +++++..
T Consensus        78 ~~a~~~~   84 (93)
T 2cqh_A           78 DYSVSKK   84 (93)
T ss_dssp             EECCCCC
T ss_pred             EEccCcc
Confidence            9998644

>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=99.78  E-value=1.7e-18  Score=120.60  Aligned_cols=82  Identities=23%  Similarity=0.290  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCceEEE
Q 030010           20 IETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN--NVQLDGKPMKI   96 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~--g~~~~g~~i~V   96 (184)
                      ..++++|||+|||++ +++++|+++|++||.|..|.|+.     .++||||+|.+.++|++||+.|+  +..|.|++|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            567899999999998 99999999999999999999974     36899999999999999999886  46799999999


Q ss_pred             EEeeCCCCCC
Q 030010           97 EIVGTNIATR  106 (184)
Q Consensus        97 ~~~~~~~~~~  106 (184)
                      ++++......
T Consensus        97 ~~a~~~~~~~  106 (112)
T 1x4f_A           97 DLSEKYKKLV  106 (112)
T ss_dssp             EEECSCSSSS
T ss_pred             EECccccccc
Confidence            9998755443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.78  E-value=2.2e-19  Score=117.81  Aligned_cols=73  Identities=23%  Similarity=0.370  Sum_probs=67.6

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc-eEE
Q 030010           23 GTKLYISNLDYGV------SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK-PMK   95 (184)
Q Consensus        23 ~~~l~V~nLp~~~------te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~-~i~   95 (184)
                      +++|||+|||..+      ++++|+++|++||.|..|.|. ..+++++|||||+|.+.++|++||+.||+..|.|+ +|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            4789999999999      779999999999999999887 34888999999999999999999999999999999 887


Q ss_pred             E
Q 030010           96 I   96 (184)
Q Consensus        96 V   96 (184)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.78  E-value=2e-18  Score=119.61  Aligned_cols=80  Identities=30%  Similarity=0.450  Sum_probs=72.5

Q ss_pred             CCCCCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ..+....++|||+|||+. +++++|+++|++||.|..|.|       +++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        21 ~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   93 (110)
T 1wf1_A           21 NDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLD   93 (110)
T ss_dssp             CCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECC
T ss_pred             CCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            344556799999999999 999999999999999999988       378999999999999999999999999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |++++...
T Consensus        94 V~~a~~~~  101 (110)
T 1wf1_A           94 INMAGEPK  101 (110)
T ss_dssp             EEESCCCC
T ss_pred             EEECCCCC
Confidence            99987533

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

Probab=99.65  E-value=1.1e-20  Score=132.38  Aligned_cols=83  Identities=23%  Similarity=0.492  Sum_probs=77.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE--------EEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKR--------YSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~--------v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      ..+.++|||+|||+.+++++|+++|++||.|..        |.|+.++ ++++++||||+|.+.++|++||+.||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            456789999999999999999999999999998        8899887 7899999999999999999999999999999


Q ss_pred             CceEEEEEeeCC
Q 030010           91 GKPMKIEIVGTN  102 (184)
Q Consensus        91 g~~i~V~~~~~~  102 (184)
                      |+.|+|+++.++
T Consensus        84 g~~l~V~~a~~~   95 (116)
T 2lcw_A           84 GNPIKVSFATRR   95 (116)
Confidence            999999998754

>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=99.78  E-value=1.3e-18  Score=121.32  Aligned_cols=82  Identities=26%  Similarity=0.441  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      +..++++|||+|||+.+++++|+++|++||.|..|.|+.+.  .+++||||+|.+.++|++||+.||+..|.|+.|.|.+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST--TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC--CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999998654  4588999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +.+.
T Consensus        82 a~~~   85 (115)
T 3lqv_A           82 YNAN   85 (115)
T ss_dssp             CCHH
T ss_pred             ecCC
Confidence            8753

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.78  E-value=3e-19  Score=127.04  Aligned_cols=83  Identities=16%  Similarity=0.299  Sum_probs=74.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE--EEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLK--RYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~--~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .......++|||+|||+.+++++|+++|++| .|.  .|.|+.++.++++|||||+|.+.++|++||+. ++..|.++.|
T Consensus        36 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I  113 (126)
T 2hgm_A           36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYI  113 (126)
T ss_dssp             TTCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEE
Confidence            3445668999999999999999999999999 677  89999988899999999999999999999975 7799999999


Q ss_pred             EEEEeeC
Q 030010           95 KIEIVGT  101 (184)
Q Consensus        95 ~V~~~~~  101 (184)
                      +|.++..
T Consensus       114 ~V~~a~~  120 (126)
T 2hgm_A          114 EVFKSSQ  120 (126)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9998864

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

Probab=99.78  E-value=5.8e-19  Score=120.39  Aligned_cols=79  Identities=20%  Similarity=0.278  Sum_probs=72.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ......++|||+|||.++++++|+++|++||.|..|+|.     ++++||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        22 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             TSCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             cCCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            334457999999999999999999999999999999987     347899999999999999999999999999999999


Q ss_pred             EeeC
Q 030010           98 IVGT  101 (184)
Q Consensus        98 ~~~~  101 (184)
                      ++++
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            9875

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=3.2e-19  Score=126.43  Aligned_cols=82  Identities=15%  Similarity=0.208  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCe----EEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDL----KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i----~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ....++|||+|||+++|+++|+++|++||.|    ..|.|+.+++++++|||||+|.+.++|++||+. |+..|.++.|.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            4567999999999999999999999999975    689999988999999999999999999999986 99999999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |..+...
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988653

>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=99.77  E-value=1.2e-18  Score=121.16  Aligned_cols=79  Identities=23%  Similarity=0.263  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ...++|||+|||+.+++++|+++|++||.|..|.|..     .++||||+|.+.++|++||+.||+..|.++.|.|+++.
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            3468999999999999999999999999999998863     46799999999999999999999999999999999998


Q ss_pred             CCCC
Q 030010          101 TNIA  104 (184)
Q Consensus       101 ~~~~  104 (184)
                      ....
T Consensus        83 ~~~~   86 (111)
T 1whx_A           83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            7543

>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=99.77  E-value=2.1e-18  Score=125.83  Aligned_cols=83  Identities=20%  Similarity=0.326  Sum_probs=76.3

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.+    ++|||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        66 ~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           66 HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             CSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCE
T ss_pred             cccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            4555667899999999999999999999999999999999866    478999999999999999999999999999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |+++.++
T Consensus       142 v~~a~~~  148 (150)
T 2i2y_A          142 VELSNGE  148 (150)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9998764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.77  E-value=5.1e-19  Score=120.88  Aligned_cols=85  Identities=21%  Similarity=0.373  Sum_probs=77.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ......++|||+|||+++++++|+++|++||.|..|.|+.+++++++|||||+|.+.++|++||+  ++..|.|+.|.|.
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~   81 (102)
T 2xs2_A            4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLG   81 (102)
T ss_dssp             CCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEE
Confidence            44456799999999999999999999999999999999999988999999999999999999997  9999999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ++.....
T Consensus        82 ~a~~~~~   88 (102)
T 2xs2_A           82 PAIRKQN   88 (102)
T ss_dssp             EEEECC-
T ss_pred             ECCcCcc
Confidence            9886543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=6.4e-19  Score=119.02  Aligned_cols=82  Identities=21%  Similarity=0.494  Sum_probs=73.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .....+.++|||+|||+.+++++|+++|++||.|..+    ..+++++|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   85 (96)
T 1fjc_A           10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3445578999999999999999999999999987655    337788999999999999999999999999999999999


Q ss_pred             EEeeCC
Q 030010           97 EIVGTN  102 (184)
Q Consensus        97 ~~~~~~  102 (184)
                      +++.+.
T Consensus        86 ~~a~~~   91 (96)
T 1fjc_A           86 YYTGEK   91 (96)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            998754

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

Probab=99.77  E-value=2e-18  Score=116.61  Aligned_cols=82  Identities=21%  Similarity=0.311  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEE-EEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRY-SIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v-~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      .....++|||+|||+++++++|+++|++||.|..| .|+.++.   .+.|||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            33457899999999999999999999999999999 4776652   2339999999999999999999999999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      ++.++.
T Consensus        88 ~a~~~~   93 (96)
T 2e44_A           88 YIPDEM   93 (96)
T ss_dssp             ECCCCC
T ss_pred             EcCccc
Confidence            998763

>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=99.77  E-value=3e-19  Score=115.24  Aligned_cols=74  Identities=14%  Similarity=0.340  Sum_probs=69.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +|||+|||+++++++|+++|++||.|..|.++.++ ++++++||||+|.+.++|++|++ +++..|.|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999887 78999999999999999999997 4889999999999874

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

Probab=99.77  E-value=3.7e-18  Score=114.99  Aligned_cols=78  Identities=17%  Similarity=0.232  Sum_probs=68.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ....++|||+|||+++++++|+++|++||.|..|  +.++ +++   ||||+|.+.++|++||+ ||+..|.|+.|+|++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456899999999999999999999999999987  4454 555   99999999999999999 999999999999998


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +....
T Consensus        79 a~~~~   83 (94)
T 2e5g_A           79 REQKE   83 (94)
T ss_dssp             SCCSC
T ss_pred             CCcCC
Confidence            76543

>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=99.76  E-value=7.3e-18  Score=123.51  Aligned_cols=82  Identities=24%  Similarity=0.440  Sum_probs=77.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ++++|||+|||+.+++++|+++|++||.|..|.++.++ ++++++||||+|.+.++|++|++.|++..+.++.|+|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            46899999999999999999999999999999999998 89999999999999999999999999999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

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

Probab=99.76  E-value=9e-18  Score=128.30  Aligned_cols=86  Identities=22%  Similarity=0.399  Sum_probs=80.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|.+|++.||+..|.|+.|+|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            456899999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 030010          100 GTNIATR  106 (184)
Q Consensus       100 ~~~~~~~  106 (184)
                      .++..+.
T Consensus       203 ~~~~~~~  209 (216)
T 2qfj_A          203 VTPPMPL  209 (216)
T ss_dssp             SSCSSTT
T ss_pred             cCCCCCC
Confidence            8765443

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.76  E-value=1e-17  Score=122.63  Aligned_cols=83  Identities=22%  Similarity=0.460  Sum_probs=78.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ....+.++|||+|||..+++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  161 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI  161 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Confidence            455678899999999999999999999999999999999997 8999999999999999999999999999999999999


Q ss_pred             EEee
Q 030010           97 EIVG  100 (184)
Q Consensus        97 ~~~~  100 (184)
                      .+++
T Consensus       162 ~~a~  165 (166)
T 3md3_A          162 NWAA  165 (166)
T ss_dssp             EESC
T ss_pred             EecC
Confidence            9986

>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=99.76  E-value=1.1e-18  Score=126.24  Aligned_cols=87  Identities=28%  Similarity=0.385  Sum_probs=75.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEE------EEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRY------SIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v------~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      .+..++++|||+|||+.+++++|+++|++||.|..+      .+....+++++|||||+|.+.++|++||+.||+..|.|
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            345678999999999999999999999999998764      22222478889999999999999999999999999999


Q ss_pred             ceEEEEEeeCCCC
Q 030010           92 KPMKIEIVGTNIA  104 (184)
Q Consensus        92 ~~i~V~~~~~~~~  104 (184)
                      +.|.|.++++...
T Consensus       120 ~~l~V~~a~~~~~  132 (143)
T 3egn_A          120 KPMVVQFARSARP  132 (143)
T ss_dssp             EECEEEECCCSCC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999986543

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.76  E-value=1.5e-17  Score=122.89  Aligned_cols=83  Identities=14%  Similarity=0.201  Sum_probs=73.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMK   95 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~   95 (184)
                      ++.....+|||+||++.+++++|+++|++||.|++|.|...+   .++||||+|.+.++|++|++.||+..|.+  +.|+
T Consensus        41 ~~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           41 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CCCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             CCCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            344556789999999999999999999999999999987543   47899999999999999999999999976  9999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |+++++..
T Consensus       118 V~~Ak~~~  125 (164)
T 1sjr_A          118 IDFSKLTS  125 (164)
T ss_dssp             EEECSSSS
T ss_pred             EEEecCCc
Confidence            99998754

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.8e-17  Score=112.26  Aligned_cols=80  Identities=23%  Similarity=0.342  Sum_probs=71.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....+.++|||+||  .+++++|+++|++||.|..|.|.     ++++||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34456799999996  89999999999999999999985     457899999999999999999999999999999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ++.+...
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9986544

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.75  E-value=2.2e-17  Score=124.51  Aligned_cols=84  Identities=26%  Similarity=0.391  Sum_probs=79.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.+..++ ++.+++||||+|.+.++|++|++.||+..|.|+.|+|++
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4678999999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +.+..
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.75  E-value=8.8e-18  Score=119.76  Aligned_cols=86  Identities=14%  Similarity=0.175  Sum_probs=72.7

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceE-EEEEecCHHHHHHHHHHhCCCccCC--
Q 030010           15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGT-AEVVYSRRADAVAAVKRYNNVQLDG--   91 (184)
Q Consensus        15 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~-afV~F~~~e~a~~Ai~~l~g~~~~g--   91 (184)
                      +.+....+-..|||+||++.+|+++|+++|++||.|.+|.|...    .++| |||+|.+.++|++|++.|||..|.+  
T Consensus        20 ~~~~~ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~   95 (130)
T 3zzy_A           20 MAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNAC   95 (130)
T ss_dssp             -----CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTE
T ss_pred             cccCCCCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCC
Confidence            34555566788899999999999999999999999999988753    2577 9999999999999999999999998  


Q ss_pred             ceEEEEEeeCCCC
Q 030010           92 KPMKIEIVGTNIA  104 (184)
Q Consensus        92 ~~i~V~~~~~~~~  104 (184)
                      +.|+|++++....
T Consensus        96 ~~LrI~~ak~~~l  108 (130)
T 3zzy_A           96 CTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEEECSCSSC
T ss_pred             cEEEEEecCCCce
Confidence            8999999987543

>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=99.75  E-value=7.5e-18  Score=123.84  Aligned_cols=82  Identities=23%  Similarity=0.367  Sum_probs=77.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ++++|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++|++.|++..+.++.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            57899999999999999999999999999999999987 88899999999999999999999999999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            644

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=1.8e-17  Score=117.45  Aligned_cols=78  Identities=23%  Similarity=0.227  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceE-EEEEecCHHHHHHHHHHhCCCccCC--ceEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGT-AEVVYSRRADAVAAVKRYNNVQLDG--KPMKIE   97 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~-afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V~   97 (184)
                      .....|||+||++.+++++|+++|++||.|..|.|.. +    .|| |||+|.+.++|+.|++.||+..|.+  +.|+|+
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~   97 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIE   97 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEE
Confidence            3345578999999999999999999999999999865 2    275 9999999999999999999999987  689999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      ++++..
T Consensus        98 ~Ak~~~  103 (124)
T 2e5i_A           98 YARPTR  103 (124)
T ss_dssp             CCSCSC
T ss_pred             EecCCc
Confidence            998754

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.74  E-value=4.5e-18  Score=113.30  Aligned_cols=77  Identities=21%  Similarity=0.354  Sum_probs=71.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ...++|||+|||+.+++++|+++|++| .|..|.|.     ++++||||+|.+.++|++||+.||+..+.|++|+|+++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            357899999999999999999999999 99999884     568899999999999999999999999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            644

>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=99.74  E-value=9.6e-18  Score=126.31  Aligned_cols=89  Identities=21%  Similarity=0.334  Sum_probs=78.1

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      +..+......++|||+|||+++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+. ++..|.|+
T Consensus         4 ~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~   82 (196)
T 1l3k_A            4 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGR   82 (196)
T ss_dssp             ----CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTE
T ss_pred             ccCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCE
Confidence            3455566778999999999999999999999999999999999998 889999999999999999999975 89999999


Q ss_pred             eEEEEEeeCCC
Q 030010           93 PMKIEIVGTNI  103 (184)
Q Consensus        93 ~i~V~~~~~~~  103 (184)
                      .|.|.++....
T Consensus        83 ~l~v~~~~~~~   93 (196)
T 1l3k_A           83 VVEPKRAVSRE   93 (196)
T ss_dssp             ECEEEECCC--
T ss_pred             EeeeecccCcc
Confidence            99999987543

>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=99.74  E-value=1.7e-17  Score=124.90  Aligned_cols=89  Identities=17%  Similarity=0.300  Sum_probs=75.0

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|.+||+. ++..|.|+.|.
T Consensus        98 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~  176 (196)
T 1l3k_A           98 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCE  176 (196)
T ss_dssp             -----CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECE
T ss_pred             cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEE
Confidence            3445567999999999999999999999999999999999998 899999999999999999999976 89999999999


Q ss_pred             EEEeeCCCCCC
Q 030010           96 IEIVGTNIATR  106 (184)
Q Consensus        96 V~~~~~~~~~~  106 (184)
                      |.++.++....
T Consensus       177 v~~a~~k~~~~  187 (196)
T 1l3k_A          177 VRKALSKQEMA  187 (196)
T ss_dssp             EEECC------
T ss_pred             EEecCChhHhc
Confidence            99998765543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.73  E-value=6.6e-18  Score=119.35  Aligned_cols=78  Identities=15%  Similarity=0.245  Sum_probs=71.2

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecC----HHH----HHHHHH--HhCCCc
Q 030010           24 TKLYISNL----DYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSR----RAD----AVAAVK--RYNNVQ   88 (184)
Q Consensus        24 ~~l~V~nL----p~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~----~e~----a~~Ai~--~l~g~~   88 (184)
                      +.|||+||    |+.+++.+|+++|++||+|..|.++.|+ |+.++|||||+|.+    +++    |.+||.  .|++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            78999999    9999999999999999999999999999 99999999999996    333    888988  789999


Q ss_pred             cCCceEEEEEeeC
Q 030010           89 LDGKPMKIEIVGT  101 (184)
Q Consensus        89 ~~g~~i~V~~~~~  101 (184)
                      |.|+.|+|.+...
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998764

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=8.7e-18  Score=117.23  Aligned_cols=80  Identities=14%  Similarity=0.155  Sum_probs=70.6

Q ss_pred             CCCCCCEEEE--cCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-----CC
Q 030010           19 AIETGTKLYI--SNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL-----DG   91 (184)
Q Consensus        19 ~~~~~~~l~V--~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~-----~g   91 (184)
                      ...++++|||  +||++.+++++|+++|++||.|..|.|..     .++||||+|.+.++|++|++.||+.+|     .+
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            3456789999  77999999999999999999999988763     267999999999999999999999988     68


Q ss_pred             ceEEEEEeeCCC
Q 030010           92 KPMKIEIVGTNI  103 (184)
Q Consensus        92 ~~i~V~~~~~~~  103 (184)
                      ++|.|.++....
T Consensus        96 ~~l~v~~a~~~p  107 (114)
T 2cq2_A           96 ITLYLNFVEKVQ  107 (114)
T ss_dssp             EECEEEEESCCC
T ss_pred             cEEEEEecccCc
Confidence            899999987543

>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=99.73  E-value=2.6e-17  Score=121.44  Aligned_cols=79  Identities=28%  Similarity=0.402  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ...++|||+|||..+++++|+++|++||.|..|.+..++ +++++|||||+|.+.++|++|++.||+..|.|+.|.|+++
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            447999999999999999999999999999999999997 8999999999999999999999999999999999999987

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.1e-17  Score=110.71  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=67.8

Q ss_pred             CCCCCE-EEEcCCCCCCCHHH----HHHHHhhC-CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           20 IETGTK-LYISNLDYGVSNED----IKELFSEV-GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        20 ~~~~~~-l~V~nLp~~~te~~----L~~~f~~~-G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ..++.+ |||+|||+.+++++    |+++|++| |+|..|      +   .|+|||+|.+.++|++|++.|++..|.|++
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------t---gG~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------T---GCSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------C---TTCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------e---cCEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            344565 99999999999988    55899999 599887      2   289999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCC
Q 030010           94 MKIEIVGTNIATR  106 (184)
Q Consensus        94 i~V~~~~~~~~~~  106 (184)
                      |+|.+++.....-
T Consensus        76 i~v~~A~~~sd~~   88 (96)
T 2diu_A           76 IIVSFTPKNRELC   88 (96)
T ss_dssp             CEEESSCCSCCCC
T ss_pred             EEEEecCCCccee
Confidence            9999998765543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.73  E-value=2.2e-17  Score=120.83  Aligned_cols=80  Identities=25%  Similarity=0.361  Sum_probs=75.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNI  103 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~  103 (184)
                      ++|||+|||.++++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++|++.|++..+.++.|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999999988899999999999999999999999999999999999987544

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.72  E-value=2.1e-17  Score=126.98  Aligned_cols=81  Identities=21%  Similarity=0.352  Sum_probs=74.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ..++|||+|||+.+++++|+++|++||.|..|+|+.++. .++|||||+|.+.++|++||+.||+..|.|++|+|.++.+
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            457899999999999999999999999999999998863 3689999999999999999999999999999999999986


Q ss_pred             CC
Q 030010          102 NI  103 (184)
Q Consensus       102 ~~  103 (184)
                      +.
T Consensus       181 ~~  182 (213)
T 4f02_A          181 RK  182 (213)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>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=99.71  E-value=1.1e-16  Score=117.60  Aligned_cols=80  Identities=29%  Similarity=0.589  Sum_probs=75.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMKI   96 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V   96 (184)
                      ..+.++|||+|||..+++++|+++|++||.|..+.+..++ ++++++||||+|.+.++|.+|++.||+..|.|  ++|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            3567899999999999999999999999999999999998 89999999999999999999999999999988  99999


Q ss_pred             EEe
Q 030010           97 EIV   99 (184)
Q Consensus        97 ~~~   99 (184)
                      .++
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>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=99.71  E-value=6.6e-17  Score=119.37  Aligned_cols=81  Identities=27%  Similarity=0.420  Sum_probs=75.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC---CceEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD---GKPMKI   96 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~---g~~i~V   96 (184)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++++++++||||+|.+.++|++|++.||+..+.   +++|+|
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            34678999999999999999999999999999999999988999999999999999999999999998776   399999


Q ss_pred             EEee
Q 030010           97 EIVG  100 (184)
Q Consensus        97 ~~~~  100 (184)
                      .++.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9873

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

Probab=99.71  E-value=3.3e-17  Score=114.28  Aligned_cols=79  Identities=18%  Similarity=0.208  Sum_probs=67.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-C---CCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-S---GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~---~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .....++|||+|||+.+++++|+++|++||.|. +.++.++ +   ++++|||||+|.+.++|++||+.|+  .++|+.|
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~   80 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLY   80 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEE
Confidence            345679999999999999999999999999999 8787776 4   6899999999999999999999883  3667666


Q ss_pred             EEEEee
Q 030010           95 KIEIVG  100 (184)
Q Consensus        95 ~V~~~~  100 (184)
                      .+..+.
T Consensus        81 ~~~~~~   86 (114)
T 2dnl_A           81 LCVSSP   86 (114)
T ss_dssp             EEECCS
T ss_pred             EeccCC
Confidence            665443

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.71  E-value=3.1e-17  Score=108.57  Aligned_cols=73  Identities=21%  Similarity=0.502  Sum_probs=67.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhC----C-------CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEV----G-------DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQ   88 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~----G-------~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~   88 (184)
                      ..+.++|||+|||+++++++|+++|++|    |       .|..+.+..+     ++||||+|.+.++|++|+ .||+..
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            3567999999999999999999999999    8       8999988744     789999999999999999 999999


Q ss_pred             cCCceEEEEE
Q 030010           89 LDGKPMKIEI   98 (184)
Q Consensus        89 ~~g~~i~V~~   98 (184)
                      |.|+.|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999873

>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=99.71  E-value=2e-17  Score=121.49  Aligned_cols=80  Identities=16%  Similarity=0.352  Sum_probs=75.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      +.++|||+|||..+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++ +++..|.|+.|+|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            46799999999999999999999999999999999997 89999999999999999999997 89999999999999987


Q ss_pred             CC
Q 030010          101 TN  102 (184)
Q Consensus       101 ~~  102 (184)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.71  E-value=3.8e-17  Score=125.29  Aligned_cols=79  Identities=16%  Similarity=0.232  Sum_probs=72.4

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLD-YGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp-~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      .++++|||+||| +.+++++|+++|++||.|..|+|+.++    +|||||+|.+.++|++||+.||+..|.|+.|+|.++
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            357899999999 899999999999999999999998653    689999999999999999999999999999999998


Q ss_pred             eCCC
Q 030010          100 GTNI  103 (184)
Q Consensus       100 ~~~~  103 (184)
                      +...
T Consensus        78 ~~~~   81 (205)
T 3tyt_A           78 KQPA   81 (205)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7543

>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=99.71  E-value=4.1e-17  Score=109.06  Aligned_cols=79  Identities=14%  Similarity=0.238  Sum_probs=62.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc--cCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQ--LDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~--~~g~~i   94 (184)
                      .....+.++|||+|||+++++++|+++|++||.|..|.|+.+    ++|||||+|.+.++|++    +++..  +.++.|
T Consensus         5 ~~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v   76 (89)
T 3d2w_A            5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISV   76 (89)
T ss_dssp             ------CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEE
Confidence            345667899999999999999999999999999999998864    68999999999999984    45544  568999


Q ss_pred             EEEEeeCCC
Q 030010           95 KIEIVGTNI  103 (184)
Q Consensus        95 ~V~~~~~~~  103 (184)
                      .|.++.++.
T Consensus        77 ~v~~a~~k~   85 (89)
T 3d2w_A           77 HISNAEPKH   85 (89)
T ss_dssp             EEEECC---
T ss_pred             EEEEcCCCC
Confidence            999987643

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

Probab=99.70  E-value=6.3e-17  Score=123.58  Aligned_cols=83  Identities=23%  Similarity=0.434  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|.|.+
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            3456899999999999999999999999999999999988 889999999999999999999999999999999999987


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +...
T Consensus       105 ~~~~  108 (216)
T 2qfj_A          105 PSNI  108 (216)
T ss_dssp             CSCC
T ss_pred             CCCc
Confidence            6643

>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=99.70  E-value=1.9e-16  Score=115.92  Aligned_cols=80  Identities=24%  Similarity=0.454  Sum_probs=73.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce--EEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP--MKI   96 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~--i~V   96 (184)
                      ....++|||+|||..+++++|+++|++||.|..+.+..++ ++.+++||||+|.+.++|.+|++.||+..|.|+.  |+|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            3457899999999999999999999999999999999988 8899999999999999999999999999999965  777


Q ss_pred             EEe
Q 030010           97 EIV   99 (184)
Q Consensus        97 ~~~   99 (184)
                      .+|
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=2.1e-16  Score=108.84  Aligned_cols=81  Identities=15%  Similarity=0.093  Sum_probs=72.7

Q ss_pred             CCCCEEEEcCCCC-----CCCHHHHHHHHhhCCCeEEEEEEeCC--CCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           21 ETGTKLYISNLDY-----GVSNEDIKELFSEVGDLKRYSIHYDR--SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        21 ~~~~~l~V~nLp~-----~~te~~L~~~f~~~G~i~~v~i~~~~--~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .++++|+|.||..     ..++++|+++|++||.|..|.|+.++  +++++||+||+|.+.++|++|++.||+..|.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            5688999999953     23689999999999999999999886  3688999999999999999999999999999999


Q ss_pred             EEEEEeeC
Q 030010           94 MKIEIVGT  101 (184)
Q Consensus        94 i~V~~~~~  101 (184)
                      |+|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>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=99.69  E-value=1.9e-17  Score=110.15  Aligned_cols=78  Identities=14%  Similarity=0.245  Sum_probs=65.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.+    +++||||+|.+.++|++|+.  ....+.++.|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            46799999999999999999999999999999998754    58899999999999986532  1355688999999887


Q ss_pred             CCCC
Q 030010          101 TNIA  104 (184)
Q Consensus       101 ~~~~  104 (184)
                      ++..
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6443

>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=99.69  E-value=2e-16  Score=125.93  Aligned_cols=84  Identities=23%  Similarity=0.437  Sum_probs=76.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHH----HHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIK----ELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~----~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      +...+.++|||+|||+.+++++|+    ++|++||.|..|.|+.  ++++++||||+|.+.++|++||+.||+..|.|+.
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            456779999999999999999976    8999999999998875  6778999999999999999999999999999999


Q ss_pred             EEEEEeeCCC
Q 030010           94 MKIEIVGTNI  103 (184)
Q Consensus        94 i~V~~~~~~~  103 (184)
                      |+|.+++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997654

>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=99.68  E-value=1.6e-16  Score=120.82  Aligned_cols=78  Identities=18%  Similarity=0.222  Sum_probs=72.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.+.+++++|||||+|.+.++|++||+.+ +..|.|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            58999999999999999999999999999999999988899999999999999999999765 4699999999998764

>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=99.68  E-value=2.4e-16  Score=116.31  Aligned_cols=81  Identities=22%  Similarity=0.422  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CC--CcceEEEEEecCHHHHHHHHHHhCCCccC---CceEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SG--RSKGTAEVVYSRRADAVAAVKRYNNVQLD---GKPMK   95 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~--~~~g~afV~F~~~e~a~~Ai~~l~g~~~~---g~~i~   95 (184)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++ ++  ++++||||+|.+.++|++|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            47899999999999999999999999999999999998 44  89999999999999999999999997776   56777


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      +.++...
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            7776643

>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=99.67  E-value=6.1e-16  Score=123.13  Aligned_cols=78  Identities=19%  Similarity=0.239  Sum_probs=71.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i~V~   97 (184)
                      ...+.++|||+|||..+++++|+++|++||.|..|+|+.++    ++||||+|.+.++|++||+.||+..|. |+.|+|+
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            34467899999999999999999999999999999998654    579999999999999999999999999 9999999


Q ss_pred             Eee
Q 030010           98 IVG  100 (184)
Q Consensus        98 ~~~  100 (184)
                      +++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            986

>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=99.67  E-value=2.5e-16  Score=122.27  Aligned_cols=82  Identities=28%  Similarity=0.383  Sum_probs=75.2

Q ss_pred             CCCCCCCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .+..++++|||+|||+ .+++++|+++|++||.|..|.|+.++    ++||||+|.+.++|++||+.|++..|.|+.|.|
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            4456789999999999 99999999999999999999998775    679999999999999999999999999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      .++....
T Consensus       105 ~~a~~~~  111 (229)
T 2adc_A          105 TLSKHQN  111 (229)
T ss_dssp             ECCSCCC
T ss_pred             EEecCcc
Confidence            9987653

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.66  E-value=3e-16  Score=116.27  Aligned_cols=80  Identities=21%  Similarity=0.502  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...+.++|||+|||..+++++|+++|++||.|..+    ..++.+++||||+|.+.++|.+|++.||+..|.|+.|+|++
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            34567899999999999999999999999987755    45788899999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +.++
T Consensus       171 a~~k  174 (175)
T 1fje_B          171 TGEK  174 (175)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            9764

>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=99.66  E-value=5.2e-16  Score=123.64  Aligned_cols=87  Identities=17%  Similarity=0.239  Sum_probs=80.5

Q ss_pred             CCCCCCCEEEEcCCCCCC-CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGV-SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~-te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ......++|||+|||+.+ ++++|+++|++||.|..|.|+.+.+++++++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus       179 ~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  258 (284)
T 3smz_A          179 PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV  258 (284)
T ss_dssp             TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Confidence            344568999999999995 9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      .++.+...
T Consensus       259 ~~a~~~~~  266 (284)
T 3smz_A          259 SFCAPGPP  266 (284)
T ss_dssp             EECCSSSC
T ss_pred             EEecCCCc
Confidence            99987554

>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=99.66  E-value=1.8e-16  Score=116.36  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=72.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ++++|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++|++  +...+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            47899999999999999999999999999999999997 89999999999999999999998  4678999999998876


Q ss_pred             C
Q 030010          101 T  101 (184)
Q Consensus       101 ~  101 (184)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.65  E-value=3.1e-16  Score=122.66  Aligned_cols=82  Identities=23%  Similarity=0.323  Sum_probs=71.4

Q ss_pred             CCCCCCCEEEEcCCCCCC---------CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 030010           18 SAIETGTKLYISNLDYGV---------SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQ   88 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~---------te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~   88 (184)
                      +.....++|||+||+..+         +|++|+++|++||.|..|.|+.     .++||||+|.+.++|+.|++.|++..
T Consensus       129 s~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          129 SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             --CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             ccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            446678999999999998         7999999999999999999985     47899999999999999999999999


Q ss_pred             c------------CCceEEEEEeeCCCC
Q 030010           89 L------------DGKPMKIEIVGTNIA  104 (184)
Q Consensus        89 ~------------~g~~i~V~~~~~~~~  104 (184)
                      |            .|+.|.|.+++....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            9            899999999987544

>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=99.65  E-value=5.2e-16  Score=124.09  Aligned_cols=84  Identities=19%  Similarity=0.329  Sum_probs=76.9

Q ss_pred             CCCCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCC--CCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           18 SAIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRS--GRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~--~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ....+.++|||+|||+. +++++|+++|++||.|..|.|+.+..  +.+++||||+|.+.++|.+|| .||+..|.|+.|
T Consensus       205 ~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i  283 (292)
T 2ghp_A          205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREI  283 (292)
T ss_dssp             --CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEE
T ss_pred             ccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEE
Confidence            35567899999999999 99999999999999999999998875  899999999999999999999 999999999999


Q ss_pred             EEEEeeCC
Q 030010           95 KIEIVGTN  102 (184)
Q Consensus        95 ~V~~~~~~  102 (184)
                      .|.++.++
T Consensus       284 ~V~~a~~k  291 (292)
T 2ghp_A          284 SVSLADKK  291 (292)
T ss_dssp             EEEECCCC
T ss_pred             EEEEecCC
Confidence            99999864

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.3e-15  Score=103.75  Aligned_cols=85  Identities=16%  Similarity=0.315  Sum_probs=71.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCC-----------HHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           17 ASAIETGTKLYISNLDYGVS-----------NEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~t-----------e~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      .....++++|+|.||.....           +++|+++|++||.|..|.| .++  .++|||||+|.+.++|++||+.||
T Consensus         9 ~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A            9 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcC
Confidence            34556789999999944332           5799999999999999965 444  378999999999999999999999


Q ss_pred             CCccCCceEEEEEeeCCCC
Q 030010           86 NVQLDGKPMKIEIVGTNIA  104 (184)
Q Consensus        86 g~~~~g~~i~V~~~~~~~~  104 (184)
                      +..|.|++|+|.++.+...
T Consensus        86 g~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             TCEETTEECEEEECCSCCC
T ss_pred             CCEECCcEEEEEEeCCCCC
Confidence            9999999999999976543

>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=99.63  E-value=2.5e-15  Score=119.65  Aligned_cols=82  Identities=22%  Similarity=0.341  Sum_probs=77.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|.+|++.|++..|.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            46899999999999999999999999999999999988 89999999999999999999999999999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      +..
T Consensus       174 ~~~  176 (284)
T 3smz_A          174 AGQ  176 (284)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            654

>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=99.62  E-value=9.9e-16  Score=117.37  Aligned_cols=78  Identities=15%  Similarity=0.281  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCe--EEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc----eE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDL--KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK----PM   94 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i--~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~----~i   94 (184)
                      .++++|||+|||+.+++++|+++|++||.|  ..|+++.++ +..+++|||+|.+.++|.+||..||+.+|.++    ++
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            467899999999999999999999999999  889888776 44569999999999999999999999999886    56


Q ss_pred             EEEEe
Q 030010           95 KIEIV   99 (184)
Q Consensus        95 ~V~~~   99 (184)
                      .|.++
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            66664

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.62  E-value=2.6e-15  Score=113.45  Aligned_cols=79  Identities=24%  Similarity=0.347  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCC-CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVG-DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPMKIE   97 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G-~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i~V~   97 (184)
                      ..++++|||+|||..+++++|+++|++|| .|..|.|+.+.    +++|||+|.+.++|.+|++.||+..|. |+.|+|.
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            35689999999999999999999999999 99999986532    679999999999999999999999999 9999999


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      +++++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.61  E-value=1e-15  Score=115.74  Aligned_cols=78  Identities=28%  Similarity=0.420  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .+++|||+|||+ .+++++|+++|++||.|..|.|+.++    ++||||+|.+.++|++|++.||+..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            368999999999 99999999999999999999998765    6799999999999999999999999999999999988


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.59  E-value=2.8e-16  Score=116.44  Aligned_cols=85  Identities=21%  Similarity=0.217  Sum_probs=72.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.+....++++++||||+|.+.++|++|| .||+..|.|+.|.|.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEe
Confidence            4556789999999999999999999999998775533332337788999999999999999999 599999999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      ++.+..
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            987643

>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=99.59  E-value=5.2e-15  Score=114.78  Aligned_cols=79  Identities=24%  Similarity=0.351  Sum_probs=72.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCC-CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVG-DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPMKIE   97 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G-~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i~V~   97 (184)
                      ..++++|||+|||..+++++|+++|++|| .|..|.|+.+    .++||||+|.+.++|.+||+.||+..|. |+.|+|.
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            35579999999999999999999999999 9999998643    3679999999999999999999999999 9999999


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      +++++
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            99864

>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=99.59  E-value=4.5e-15  Score=117.33  Aligned_cols=83  Identities=27%  Similarity=0.369  Sum_probs=75.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccC---CceEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN-VQLD---GKPMKIE   97 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g-~~~~---g~~i~V~   97 (184)
                      ++++|||+|||..+++++|+++|++||.|..|.|+.+.+++++|||||+|.+.++|.+||..||+ ..+.   +++|.|.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999955 4444   8999999


Q ss_pred             EeeCCCC
Q 030010           98 IVGTNIA  104 (184)
Q Consensus        98 ~~~~~~~  104 (184)
                      ++.....
T Consensus       175 ~~~~~~~  181 (261)
T 3sde_A          175 PMEQFDD  181 (261)
T ss_dssp             ECCCEES
T ss_pred             eccccCc
Confidence            9886543

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.59  E-value=6.4e-16  Score=106.25  Aligned_cols=72  Identities=24%  Similarity=0.403  Sum_probs=63.5

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           28 ISNLDYGVSNEDIKELF------------SEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        28 V~nLp~~~te~~L~~~f------------~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +.+|++.+++++|+++|            ++||.|..|.|+.+++++++|||||+|.+.++|++|++.||+..|.|++|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            45666667777776666            999999999999888888999999999999999999999999999999999


Q ss_pred             EEEe
Q 030010           96 IEIV   99 (184)
Q Consensus        96 V~~~   99 (184)
                      |+++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.59  E-value=4.9e-15  Score=101.98  Aligned_cols=81  Identities=15%  Similarity=0.142  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHHhhCCCeEEEEEEeCCC---CCcceEEEEEecCHHHHHHHHHHhCCC
Q 030010           21 ETGTKLYISNL--DYGVS--------NEDIKELFSEVGDLKRYSIHYDRS---GRSKGTAEVVYSRRADAVAAVKRYNNV   87 (184)
Q Consensus        21 ~~~~~l~V~nL--p~~~t--------e~~L~~~f~~~G~i~~v~i~~~~~---~~~~g~afV~F~~~e~a~~Ai~~l~g~   87 (184)
                      .+++.|.|.|+  |..+.        +++|+++|++||.|..|.|+.++.   .+++|++||+|.+.++|++|++.||+.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46889999998  43443        368999999999999999988873   367999999999999999999999999


Q ss_pred             ccCCceEEEEEeeC
Q 030010           88 QLDGKPMKIEIVGT  101 (184)
Q Consensus        88 ~~~g~~i~V~~~~~  101 (184)
                      .|.|+.|+|+++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999864

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.58  E-value=7.1e-15  Score=103.22  Aligned_cols=80  Identities=15%  Similarity=0.212  Sum_probs=70.4

Q ss_pred             CCCEEEEcCCC--CCC---CHHHHHHHHhhCCCeEEEEEEeCC-C----CCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           22 TGTKLYISNLD--YGV---SNEDIKELFSEVGDLKRYSIHYDR-S----GRSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        22 ~~~~l~V~nLp--~~~---te~~L~~~f~~~G~i~~v~i~~~~-~----~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      ++++|+|.|+-  .++   .+++|+++|++||.|..|.|+.++ +    ++++|++||+|.+.++|++|++.||+..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            68999999983  222   368999999999999999999876 2    4578999999999999999999999999999


Q ss_pred             ceEEEEEeeC
Q 030010           92 KPMKIEIVGT  101 (184)
Q Consensus        92 ~~i~V~~~~~  101 (184)
                      +.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=99.58  E-value=3.9e-15  Score=118.97  Aligned_cols=82  Identities=16%  Similarity=0.259  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCC-CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVG-DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G-~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||+.+++++|+++|++|| .|..|.|+.++.+.+++||||+|.+.++|.+|++.|++..|.|+.|.|.++.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            578999999999999999999999999 9999999988888889999999999999999999999999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      +..
T Consensus       196 ~~~  198 (292)
T 2ghp_A          196 PLE  198 (292)
T ss_dssp             CC-
T ss_pred             CCc
Confidence            544

>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=99.58  E-value=6.4e-15  Score=116.47  Aligned_cols=81  Identities=22%  Similarity=0.380  Sum_probs=73.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .......++|||+|||+++|+++|+++|++||.|..|.|..+     ++||||+|.+.++|++||..||+..|.++.|.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            344566789999999999999999999999999999998643     689999999999999999999999999999999


Q ss_pred             EEeeCC
Q 030010           97 EIVGTN  102 (184)
Q Consensus        97 ~~~~~~  102 (184)
                      .++.+.
T Consensus        91 ~~a~~~   96 (261)
T 3sde_A           91 RFATHG   96 (261)
T ss_dssp             EECCCS
T ss_pred             eecccC
Confidence            998753

>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=99.56  E-value=1.6e-14  Score=106.37  Aligned_cols=75  Identities=19%  Similarity=0.443  Sum_probs=67.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhC----C-------CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEV----G-------DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~----G-------~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      .+.++|||+|||+.+++++|+++|++|    |       .|..+.+..     .++||||+|.+.++|++|+ .||+..|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-----CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            357899999999999999999999999    6       777777753     4789999999999999999 8999999


Q ss_pred             CCceEEEEEeeC
Q 030010           90 DGKPMKIEIVGT  101 (184)
Q Consensus        90 ~g~~i~V~~~~~  101 (184)
                      .|+.|.|.++..
T Consensus        76 ~g~~i~v~~~~~   87 (172)
T 2g4b_A           76 QGQSLKIRRPHD   87 (172)
T ss_dssp             TTEECEEECCSS
T ss_pred             cCceeeecCCcc
Confidence            999999998654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.54  E-value=2.3e-14  Score=107.87  Aligned_cols=76  Identities=18%  Similarity=0.431  Sum_probs=66.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhC----C-------CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEV----G-------DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~----G-------~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      .+++|||+|||+.+++++|+++|++|    |       .|..+.+.     ++++||||+|.+.++|++|| .||+..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            47899999999999999999999999    5       66666664     44789999999999999999 89999999


Q ss_pred             CceEEEEEeeCCC
Q 030010           91 GKPMKIEIVGTNI  103 (184)
Q Consensus        91 g~~i~V~~~~~~~  103 (184)
                      |+.|.|.++....
T Consensus        77 g~~i~v~~~~~~~   89 (198)
T 2yh0_A           77 GQSLKIRRPHDYQ   89 (198)
T ss_dssp             TEEEEEECCCCCC
T ss_pred             CceEEEeCCCCCC
Confidence            9999999887643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.2e-13  Score=92.85  Aligned_cols=78  Identities=22%  Similarity=0.237  Sum_probs=64.3

Q ss_pred             CCCCEEEEcCCC-------CCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           21 ETGTKLYISNLD-------YGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        21 ~~~~~l~V~nLp-------~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ....+|.|.-..       ..+++++|+++|++||.|..|.|+    ++++|||||+|.+.++|+.||+.++  .+.+++
T Consensus         8 ~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~   81 (100)
T 2d9o_A            8 QGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNP   81 (100)
T ss_dssp             CSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSB
T ss_pred             CccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCe
Confidence            335677776543       458999999999999999999987    3678999999999999999998744  467999


Q ss_pred             EEEEEeeCCCC
Q 030010           94 MKIEIVGTNIA  104 (184)
Q Consensus        94 i~V~~~~~~~~  104 (184)
                      |+|.++++...
T Consensus        82 l~V~~a~~~~~   92 (100)
T 2d9o_A           82 LKISWLEGQPQ   92 (100)
T ss_dssp             CEEECSSCCCC
T ss_pred             EEEEEccCCCC
Confidence            99999876543

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.49  E-value=5.9e-14  Score=115.08  Aligned_cols=78  Identities=17%  Similarity=0.232  Sum_probs=66.3

Q ss_pred             CCCCCCCEEEEcC--CCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC---Cc
Q 030010           18 SAIETGTKLYISN--LDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD---GK   92 (184)
Q Consensus        18 ~~~~~~~~l~V~n--Lp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~---g~   92 (184)
                      ....++.+|||+|  |++.+||++|+++|++||+|..|.+..     .++||||+|.+.++|++||+.||+.++.   |+
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            3467789999999  578999999999999999999887653     4689999999999999999999998873   34


Q ss_pred             --eEEEEEee
Q 030010           93 --PMKIEIVG  100 (184)
Q Consensus        93 --~i~V~~~~  100 (184)
                        .|.|.++.
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence              57777764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=7.9e-13  Score=92.78  Aligned_cols=81  Identities=22%  Similarity=0.285  Sum_probs=72.6

Q ss_pred             CCCCCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecC-HHHHHHHHHHhC--CCccCCc
Q 030010           17 ASAIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR-RADAVAAVKRYN--NVQLDGK   92 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~-~e~a~~Ai~~l~--g~~~~g~   92 (184)
                      .....+++.|||+||+.. +++++|+++|++||+|..|.+..+..     .|||+|.+ .++|..|++.|+  +..|.+.
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            456788999999999999 99999999999999999999987754     69999999 899999999995  6899999


Q ss_pred             eEEEEEeeCC
Q 030010           93 PMKIEIVGTN  102 (184)
Q Consensus        93 ~i~V~~~~~~  102 (184)
                      .+++++....
T Consensus        87 ~~~~evL~Ge   96 (121)
T 1owx_A           87 EVTWEVLEGE   96 (121)
T ss_dssp             SEEEEECCHH
T ss_pred             EEEEEECCCH
Confidence            9999887643

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.44  E-value=6e-13  Score=92.79  Aligned_cols=78  Identities=19%  Similarity=0.196  Sum_probs=66.2

Q ss_pred             CCCCEEEEcCC--CCCC--------CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           21 ETGTKLYISNL--DYGV--------SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        21 ~~~~~l~V~nL--p~~~--------te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      .++++|.|.|+  +...        .+++|+++|++||.|..|.|..+.   .+|++||+|.+.++|++|++.|||..|.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            46889999998  2221        135789999999999999886543   4899999999999999999999999999


Q ss_pred             CceEEEEEeeC
Q 030010           91 GKPMKIEIVGT  101 (184)
Q Consensus        91 g~~i~V~~~~~  101 (184)
                      |+.|+|+++..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999865

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=1.4e-11  Score=81.72  Aligned_cols=75  Identities=13%  Similarity=0.235  Sum_probs=62.5

Q ss_pred             CCCCEEEEcCCCC----CCCH----HHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           21 ETGTKLYISNLDY----GVSN----EDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        21 ~~~~~l~V~nLp~----~~te----~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ++.-+|+|.-++.    +...    .+|.+.|++||.|..++|+.++       +||+|.+.++|.+||+ ||+..+.|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            3456777776652    2222    5789999999999999998763       8999999999999998 999999999


Q ss_pred             eEEEEEeeCCC
Q 030010           93 PMKIEIVGTNI  103 (184)
Q Consensus        93 ~i~V~~~~~~~  103 (184)
                      .|+|+++++..
T Consensus        77 ~LkV~lkt~dW   87 (91)
T 2dnr_A           77 TITIALKSPSG   87 (91)
T ss_dssp             EEEEEECCCSS
T ss_pred             EEEEEeCCCCc
Confidence            99999998754

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=1.5e-10  Score=77.11  Aligned_cols=74  Identities=9%  Similarity=0.189  Sum_probs=61.9

Q ss_pred             CCCCCEEEEcCCCCC------CCH---HHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           20 IETGTKLYISNLDYG------VSN---EDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~------~te---~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      .++.-+|+|.-++..      ..+   .+|.+.|++||.|..++|+.++       +||+|.+.++|.+||+ ||+..+.
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            445678888877632      221   4689999999999999999763       9999999999999998 9999999


Q ss_pred             CceEEEEEeeC
Q 030010           91 GKPMKIEIVGT  101 (184)
Q Consensus        91 g~~i~V~~~~~  101 (184)
                      |+.|+|.+..+
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998653

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.06  E-value=4.8e-10  Score=86.22  Aligned_cols=79  Identities=15%  Similarity=0.187  Sum_probs=65.3

Q ss_pred             CCEEEEcCCC-----CCCCHHHHHHHHhhCCCeEEEEEEeCC-----CCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           23 GTKLYISNLD-----YGVSNEDIKELFSEVGDLKRYSIHYDR-----SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        23 ~~~l~V~nLp-----~~~te~~L~~~f~~~G~i~~v~i~~~~-----~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ...+.+.|+-     ..-.+++|++.|++||.|..|.|+.+.     +++++|++||+|.+.++|++||+.|||..+.|+
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            4455555541     123467899999999999999998554     348899999999999999999999999999999


Q ss_pred             eEEEEEeeC
Q 030010           93 PMKIEIVGT  101 (184)
Q Consensus        93 ~i~V~~~~~  101 (184)
                      .|.|.+...
T Consensus       204 ~i~~~~~~~  212 (222)
T 3dxb_A          204 KVVAEVYDQ  212 (222)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.63  E-value=2.1e-07  Score=63.31  Aligned_cols=73  Identities=21%  Similarity=0.211  Sum_probs=65.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhC-----CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEV-----GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~-----G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +..++|-|-|||.+++...|+.++.++     |.|.+|.+..|.     +-|+|+|.+...|-+|.-.|+|.+|.|++|+
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-----~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-----NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-----TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-----CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            346788888999999999999999999     999999888774     3699999999999999989999999999999


Q ss_pred             EEE
Q 030010           96 IEI   98 (184)
Q Consensus        96 V~~   98 (184)
                      +.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            864

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.15  E-value=0.00012  Score=49.14  Aligned_cols=75  Identities=15%  Similarity=0.207  Sum_probs=62.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhC-----CCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEV-----GDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~-----G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      .....++|.|.|||..+.++.|+-+|+.-     |.|..|+...       .-|+|+|.+.+.|++.++. ..+.|++..
T Consensus         4 ~~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~~~   75 (104)
T 2dhx_A            4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHGAQ   75 (104)
T ss_dssp             SCCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSSSB
T ss_pred             CccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecCeE
Confidence            44568999999999999999999999862     6888887753       4799999999999999863 478999999


Q ss_pred             EEEEEeeC
Q 030010           94 MKIEIVGT  101 (184)
Q Consensus        94 i~V~~~~~  101 (184)
                      |.|....+
T Consensus        76 LsV~P~~~   83 (104)
T 2dhx_A           76 LSLRPAPP   83 (104)
T ss_dssp             CEEEECCC
T ss_pred             EEEEcCCC
Confidence            99976544

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=98.04  E-value=3.7e-05  Score=51.16  Aligned_cols=58  Identities=22%  Similarity=0.228  Sum_probs=49.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY   84 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l   84 (184)
                      .....+.++| .+|.++...||.++|+.||.| .|+++.|.      .|||.|.+++.|..|+..+
T Consensus        12 ~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           12 QPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC------eEEEEecCHHHHHHHHHhc
Confidence            3444678888 999999999999999999965 47777664      7999999999999999865

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.98  E-value=1.9e-05  Score=53.34  Aligned_cols=77  Identities=18%  Similarity=0.186  Sum_probs=62.6

Q ss_pred             CCCCEEEEcCCCCCC-C----HHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           21 ETGTKLYISNLDYGV-S----NEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~-t----e~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .-.++|+|.||+..+ .    .+.++++|.+|+++....+...     -.-.-|.|.+.++|.+|-..||+..+.|+.|+
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            346789999998865 2    2568999999998877655522     22578999999999999999999999999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |-++.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998853

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.97  E-value=5.4e-05  Score=50.06  Aligned_cols=69  Identities=13%  Similarity=0.215  Sum_probs=57.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CC--CcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SG--RSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~--~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      ++|.|++||+.+||+++.+.++.+..+....++..+ +.  ....-|||.|.+.+++..-.+.++++.|.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            578999999999999999999988887777776655 22  2456899999999999999999999887653

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.59  E-value=0.00014  Score=48.47  Aligned_cols=55  Identities=24%  Similarity=0.225  Sum_probs=47.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      .+.++| .+|.++...||.++|+.||. ..|.++.|.      .|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            466777 99999999999999999994 458888764      79999999999999998764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.33  E-value=0.00081  Score=46.45  Aligned_cols=74  Identities=9%  Similarity=0.081  Sum_probs=56.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-ceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG-KPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g-~~i~V~   97 (184)
                      .....+.|.|-+.|... -..|-..|++||.|.+....     ....+.+|.|.+..+|++||. .|+..|.+ -.|-|.
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~-----~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC-----CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            34457788888998874 56778899999999887652     123489999999999999996 49998885 445555


Q ss_pred             Ee
Q 030010           98 IV   99 (184)
Q Consensus        98 ~~   99 (184)
                      ..
T Consensus        93 p~   94 (119)
T 1wwh_A           93 PC   94 (119)
T ss_dssp             EC
T ss_pred             EC
Confidence            43

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.24  E-value=0.00044  Score=46.04  Aligned_cols=78  Identities=14%  Similarity=0.189  Sum_probs=55.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCC--cceEEEEEecCHHHHHHHHHHhCCCccCCc-----e
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGR--SKGTAEVVYSRRADAVAAVKRYNNVQLDGK-----P   93 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~--~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~-----~   93 (184)
                      -+-+|.|+.||+.+||+++.+.++..=.+....++..+ +.+  ...-|||.|.+.+++..-.+.+++..|.+.     +
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            35689999999999999988877765444332222222 211  234689999999999999999999777653     3


Q ss_pred             EEEEEe
Q 030010           94 MKIEIV   99 (184)
Q Consensus        94 i~V~~~   99 (184)
                      ..|++|
T Consensus        88 a~VE~A   93 (97)
T 2l08_A           88 AVVEFA   93 (97)
T ss_dssp             EEEEEC
T ss_pred             eEEEec
Confidence            445554

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.62  E-value=0.0012  Score=56.01  Aligned_cols=54  Identities=11%  Similarity=0.070  Sum_probs=40.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHH
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK   82 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~   82 (184)
                      ++|+|. .|..+++.+|.++|++||+|..+.+..++    .-|+.|||.+.+++.+++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHh
Confidence            789997 79999999999999999999998776543    3599999999999887764

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.32  E-value=0.0041  Score=44.38  Aligned_cols=36  Identities=22%  Similarity=0.222  Sum_probs=28.7

Q ss_pred             EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 030010           53 YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL   89 (184)
Q Consensus        53 v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~   89 (184)
                      ++|+.+.. +++||+||+|.+.++|++|++.+++...
T Consensus         3 ~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~   38 (158)
T 2kn4_A            3 YKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNG   38 (158)
T ss_dssp             EEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             EEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCC
Confidence            55665553 5899999999999999999998876433

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.18  E-value=0.009  Score=41.81  Aligned_cols=77  Identities=13%  Similarity=0.218  Sum_probs=53.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEe---------CCCC-----CcceEEEEEecCHHHHHHHHHHhCCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHY---------DRSG-----RSKGTAEVVYSRRADAVAAVKRYNNV   87 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~---------~~~~-----~~~g~afV~F~~~e~a~~Ai~~l~g~   87 (184)
                      .+.|.|-+.|+..+ ..+-+.|++||.|.+ +....         .+..     ....+..|+|.+..+|++||. .|+.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45566778877644 556678999999865 21110         0000     124588999999999999996 5999


Q ss_pred             ccCCceEEEEEeeC
Q 030010           88 QLDGKPMKIEIVGT  101 (184)
Q Consensus        88 ~~~g~~i~V~~~~~  101 (184)
                      .|.|.-|-|....+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99998777776643

>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=95.32  E-value=0.0048  Score=43.76  Aligned_cols=40  Identities=23%  Similarity=0.233  Sum_probs=35.9

Q ss_pred             CCcceEEEEEecCHHHHHHHHHHh-CCCccCCceEEEEEeeC
Q 030010           61 GRSKGTAEVVYSRRADAVAAVKRY-NNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        61 ~~~~g~afV~F~~~e~a~~Ai~~l-~g~~~~g~~i~V~~~~~  101 (184)
                      .+.+|+++|+|.+.++|++|++.| |+..++| .|.+.++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            357899999999999999999999 9999999 899887654

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.56  E-value=0.29  Score=41.87  Aligned_cols=56  Identities=23%  Similarity=0.249  Sum_probs=45.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNN   86 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g   86 (184)
                      .+.++|+ +|..+...+|.++|+.||.| .|.++.+.      .|||.|.+.+.|..++..+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt------~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS------EEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC------eEEEEECCHHHHHHHHHHHHh
Confidence            4666776 88888999999999999964 46665432      799999999999999998753

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=84.28  E-value=3.1  Score=25.46  Aligned_cols=68  Identities=18%  Similarity=0.242  Sum_probs=41.6

Q ss_pred             EEEEcCC-CCCCCHHHHHHHHhhCC-----CeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           25 KLYISNL-DYGVSNEDIKELFSEVG-----DLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        25 ~l~V~nL-p~~~te~~L~~~f~~~G-----~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ++||..= -..+...+|..++..-+     .|-.|.|..       .|.||+-.. +.+..+++.|+...+.|+.+.|+.
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d-------~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~   73 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMD-------NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNK   73 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECS-------SCEEEEECT-TCHHHHHHHHTTCCC---CCCEEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeC-------CcEEEEECH-HHHHHHHHHhccccCcCceEEEEE
Confidence            4555311 23356677777776443     455666653       278888874 567888999999999999999987


Q ss_pred             ee
Q 030010           99 VG  100 (184)
Q Consensus        99 ~~  100 (184)
                      ++
T Consensus        74 ~~   75 (76)
T 2g0c_A           74 AN   75 (76)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

---

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	184
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-15
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-12
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	8e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001

>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 = 73.0 bits (179), Expect = 3e-18
 Identities = 46/75 (61%), Positives = 63/75 (84%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KL +SNLD+GVS+ DI+ELF+E G LK+ ++HYDRSGRS GTA+V + R+ADA+ A+K+Y
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 85 NNVQLDGKPMKIEIV 99
          N V LDG+PM I++V
Sbjct: 62 NGVPLDGRPMNIQLV 76

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.4 bits (172), Expect = 5e-17
 Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 21  ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR--SGRSKGTAEVVYSRRADAV 78
           +T +K+ + N+ +  +  +I+ELFS  G+LK   +      +G  +G   V +  + DA 
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 79  AAVKR-YNNVQLDGKPMKIEIVGTNIATR 106
            A     ++  L G+ + +E   + +  +
Sbjct: 66  KAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.3 bits (164), Expect = 6e-16
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADA 77
           ++    LY+ NL +  + E I ELFS+ GD+K+  +  D+    + G   V Y  RADA
Sbjct: 3  LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 62

Query: 78 VAAVKRYNNVQLDGKPMKIE 97
            A++  N  +LD + ++ +
Sbjct: 63 ENAMRYINGTRLDDRIIRTD 82

>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 = 65.4 bits (159), Expect = 3e-15
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 9/90 (10%)

Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR----SGRSKGTAEVVYSRRADAVAAV 81
           L+I NL++  + E +K +FS+VG +K  +I   +       S G   V Y +   A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 82  KRYNNVQLDGKPMKIEIVGTNIATRTAAPA 111
           K+     +DG  +++      I+ R   PA
Sbjct: 61  KQLQGHTVDGHKLEVR-----ISERATKPA 85

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 5e-15
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSI-HYDRSGRSKGTAEVVYSRRADAVAAVKR 83
           LY+ +L   V+   + E FS  G +    +     + RS G A V + + ADA  A+  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 84 YNNVQLDGKPMKIEI 98
           N   + GKP++I  
Sbjct: 62 MNFDVIKGKPVRIMW 76

>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 = 64.6 bits (157), Expect = 6e-15
 Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAA 80
          + T L ++ L   +++ ++  LF  +G +     +   ++G S G A V ++   D+  A
Sbjct: 1  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 81 VKRYNNVQLDGKPMKIEI 98
          +K  N + +  K +K+  
Sbjct: 61 IKVLNGITVRNKRLKVSY 78

>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 = 65.0 bits (158), Expect = 8e-15
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAA 80
          E    LYI NL Y ++ E++ ++F + G +++       +  ++GTA VVY    DA  A
Sbjct: 5  EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI--RVGNTPETRGTAYVVYEDIFDAKNA 62

Query: 81 VKRYNNVQLDGKPMKIEI 98
              +   +  + + +  
Sbjct: 63 CDHLSGFNVCNRYLVVLY 80

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 1e-14
 Identities = 18/84 (21%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
          +G + +  T  +L++SN+ +   + D++++F + G +    I ++    SKG   V +  
Sbjct: 2  SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFEN 60

Query: 74 RADAVAAVKRYNNVQLDGKPMKIE 97
           ADA  A ++ +   ++G+ +++ 
Sbjct: 61 SADADRAREKLHGTVVEGRKIEVN 84

>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 = 63.2 bits (153), Expect = 2e-14
 Identities = 26/83 (31%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSR 73
          G  +  +    L +  L    +  D++E+FS+ G +   SI YD +S RS+G A V +  
Sbjct: 1  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 74 RADAVAAVKRYNNVQLDGKPMKI 96
            DA  A +R N ++LDG+ +++
Sbjct: 61 VDDAKEAKERANGMELDGRRIRV 83

>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 = 62.3 bits (151), Expect = 4e-14
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
          K++I  L +  + E ++E F + G++K   +  D  + RS+G   V +  +A     + +
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 84 YNNVQLDGKPMKIEI 98
           +  +LD K +  ++
Sbjct: 62 -SRHELDSKTIDPKV 75

>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 = 62.3 bits (151), Expect = 5e-14
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLK-RYSIHYDRSGRSKGTAEVVYSRRADAVAAV 81
           T LY++NL   ++++ +  +F + G +  +  +    +GR +G A V Y++R +A  A+
Sbjct: 6  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 82 KRYNNVQLDGKPMKIEI 98
             NNV  +G    + +
Sbjct: 66 SALNNVIPEGGSQPLSV 82

>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 = 61.6 bits (149), Expect = 8e-14
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSG-RSKGTAEVVYSRRAD 76
          SA      LY+S L   ++ +++++LFS+ G +    I  D+    S+G   + + +R +
Sbjct: 1  SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 60

Query: 77 AVAAVKRYNNVQLDGKPMKIEI 98
          A  A+K  N  +  G    I +
Sbjct: 61 AEEAIKGLNGQKPSGATEPITV 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 8e-14
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD-RSGRSKGTAEVVYSRRADAVAA 80
          T   LY+  L   V ++ +   F   GD+    I  D  + + +G A V +    DA AA
Sbjct: 4  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 81 VKRYNNVQLDGKPMKIEI 98
          +   N  +L G+ +++ +
Sbjct: 64 IDNMNESELFGRTIRVNL 81

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 9e-14
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSI---HYDRSGRSKGTAEVVYSRRADAVAA 80
           +L+I  +      E+I E  ++V +     I         +++G A V Y     A  A
Sbjct: 2  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 81 VKRYNN--VQLDGKPMKIE 97
           ++     +QL G  + ++
Sbjct: 62 RRKLMPGRIQLWGHQIAVD 80

>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 = 61.7 bits (149), Expect = 9e-14
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDL-KRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
          T L ++ L   ++ E+ + LF  +G++     +    +G+S G   V Y    DA  A+ 
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 83 RYNNVQLDGKPMKIE 97
            N ++L  K +K+ 
Sbjct: 63 TLNGLRLQTKTIKVS 77

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 4e-13
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
          KL+I  L   ++++ +KEL +  G LK +++  D  +G SKG A   Y        A+  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 84 YNNVQLDGKPMKIE 97
           N +QL  K + ++
Sbjct: 63 LNGMQLGDKKLLVQ 76

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 8e-13
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          +    + ++NL       D++ELF   G + R  +  D+ +G+SKG A + + RR DA  
Sbjct: 6  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 80 AVKRYNNVQLDGKPMKIE 97
          A+   +    D   + +E
Sbjct: 66 AIAGVSGFGYDHLILNVE 83

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (143), Expect = 8e-13
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAV 81
              +Y   +  G++++ +++ FS  G +    +        KG + V +S    A  A+
Sbjct: 17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAI 71

Query: 82 KRYNNVQLDGKPMKIE 97
             N   ++G  +K  
Sbjct: 72 VSVNGTTIEGHVVKCY 87

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 1e-12
 Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADA 77
          A++  + L +  L +  + +D+KE FS  G++    +  D  +G SKG   V ++     
Sbjct: 4  AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 78 VAAVKRYNNVQLDGKPMKIEI 98
          V  + + +   +DG+    ++
Sbjct: 64 VKVMSQRH--MIDGRWCDCKL 82

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 58.1 bits (140), Expect = 2e-12
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRAD 76
          +  +     L   NL + ++ +++KE+F +            + G+SKG A + +   AD
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLVSQDGKSKGIAYIEFKSEAD 65

Query: 77 AVAAVKRYNNVQLDGKPMKIEI 98
          A   ++     ++DG+ + +  
Sbjct: 66 AEKNLEEKQGAEIDGRSVSLYY 87

>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 = 57.9 bits (139), Expect = 2e-12
 Identities = 12/76 (15%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLK-RYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
            L+++N     +  +I++L  ++  +     +   R   S+  A +  + + DA   V+
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 83 RYNNVQLDGKPMKIEI 98
          + N ++++G  +  ++
Sbjct: 62 KLNGLKIEGYTLVTKV 77

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 57.8 bits (139), Expect = 3e-12
 Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSG-RSKGTAEVVYSRRADAVAAV 81
          G  L+++++      ++I+E F + G++K   ++ DR    SKG A V Y     A+AA 
Sbjct: 7  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 82 KRYNNVQLDGKPMKIE 97
          +  N  ++ G+ ++++
Sbjct: 67 EALNGAEIMGQTIQVD 82

>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 = 57.7 bits (139), Expect = 3e-12
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSI-HYDRSGRSKGTAEVVYSRRADAVAAVK 82
            +Y+  LD  VS   + ELF + G +    +     +G+ +G   V +    DA  A+K
Sbjct: 10 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 83 RYNNVQLDGKPMKIE 97
            + ++L GKP+++ 
Sbjct: 70 IMDMIKLYGKPIRVN 84

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.4 bits (138), Expect = 3e-12
 Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 15 GRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLK-RYSIHYDRSGRSKGTAEVVYSR 73
          G +S     T + + N+ + VS ++I + F     +     + Y+  G   G A V +  
Sbjct: 1  GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 74 RADAVAAVKRYNNVQLDGKPMKIEI 98
          R +A AAV   N+  +  + +K+ +
Sbjct: 61 RDEATAAVIDLNDRPIGSRKVKLVL 85

>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 = 57.7 bits (139), Expect = 3e-12
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          ++L++ NL   ++ E++++LF + G      IH D+         +    R  A  A   
Sbjct: 9  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKVE 63

Query: 84 YNNVQLDGKPMKIEI 98
           +N+ L GK +++  
Sbjct: 64 LDNMPLRGKQLRVRF 78

>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 = 57.8 bits (139), Expect = 4e-12
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRS-GRSKGTAEVVYS 72
          AG       G  L+I +L     ++D+ ++F   G++    +  D+    SK    V Y 
Sbjct: 9  AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 68

Query: 73 RRADAVAAVKRYNNVQLDGKPMKIEI 98
              A AA++  N  Q+  K +K+++
Sbjct: 69 NPVSAQAAIQSMNGFQIGMKRLKVQL 94

>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 = 57.1 bits (137), Expect = 4e-12
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSI--HYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          ++I NLD  +  + + + FS  G + +         +G SKG A + ++    + AA++ 
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 84 YNNVQLDGKPMKIEI 98
           N   L  +P+ +  
Sbjct: 61 MNGQYLCNRPITVSY 75

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.5 bits (138), Expect = 5e-12
 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 2/93 (2%)

Query: 5  QVSAFPVQQAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSK 64
          + S    Q A +    +  T LYISNL   +  ++++ +    G +    I  D SG S+
Sbjct: 2  KASGVQAQMAKQQE--QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 59

Query: 65 GTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE 97
          G             A +  +N   +   P    
Sbjct: 60 GVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA 92

>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 = 57.0 bits (137), Expect = 5e-12
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
            ++I NLD  + N+ + + FS  G++    +  D +G SKG   V +  +  A  A+++
Sbjct: 9  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEK 67

Query: 84 YNNVQLDGKPMKIE 97
           N + L+ + + + 
Sbjct: 68 MNGMLLNDRKVFVG 81

>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 = 57.0 bits (137), Expect = 8e-12
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
            ++   L   +   D+++ FS VG ++   I  DR S RSKG A V +        A+ 
Sbjct: 19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 78

Query: 83 RYNNVQLDGKPMKIEI 98
               +L G P+ ++ 
Sbjct: 79 -LTGQRLLGVPIIVQA 93

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 1e-11
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
            LY+ NL   V+   I +LFS++G  K   +  +    +     V +    DA AA+  
Sbjct: 9  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-TSNDPYCFVEFYEHRDAAAALAA 67

Query: 84 YNNVQLDGKPMKIE 97
           N  ++ GK +K+ 
Sbjct: 68 MNGRKILGKEVKVN 81

>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 = 55.8 bits (134), Expect = 2e-11
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRA 75
          R  A     ++Y+ NL   +  +DI+++F + G ++   I           A V +    
Sbjct: 7  RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD--IDLKNRRGGPPFAFVEFEDPR 64

Query: 76 DAVAAVKRYNNVQLDGKPMKIEI 98
          DA  AV   +    DG  +++E 
Sbjct: 65 DAEDAVYGRDGYDYDGYRLRVEF 87

>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 = 55.5 bits (133), Expect = 3e-11
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          E   KL+I  L +  + E ++  + + G L    +  D  S RS+G   V +S  A+  A
Sbjct: 18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 80 AVKRYNNVQLDGKPMKIE 97
          A+       +DG+ ++ +
Sbjct: 78 AMA-ARPHSIDGRVVEPK 94

>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 = 55.0 bits (132), Expect = 3e-11
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          E   KL+I  L +  ++E ++  F + G L    +  D  + RS+G   V Y+   +  A
Sbjct: 4  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 80 AVKRYNNVQLDGKPMKIE 97
          A+      ++DG+ ++ +
Sbjct: 64 AMNA-RPHKVDGRVVEPK 80

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 4e-11
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAV 78
           + +   LY+ NL    S E I++ F+            +R  + +  A V +S R DAV
Sbjct: 4  TMSSVKILYVRNLMLSTSEEMIEKEFN-----NIKPGAVERVKKIRDYAFVHFSNREDAV 58

Query: 79 AAVKRYNNVQLDGKPMKIEI 98
           A+K  N   LDG P+++ +
Sbjct: 59 EAMKALNGKVLDGSPIEVTL 78

>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 = 54.2 bits (130), Expect = 4e-11
 Identities = 17/74 (22%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
          K++I  L +  + +D+K+ FS+ G++   ++  D  +GRS+G   V++         + +
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 84 YNNVQLDGKPMKIE 97
              +L+GK +  +
Sbjct: 61 -KEHKLNGKVIDPK 73

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 5e-11
 Identities = 10/75 (13%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKR 83
          K+++  L      E I+E F   G+++   +  D  + + +G   + +         +++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 84 YNNVQLDGKPMKIEI 98
               +     +I++
Sbjct: 61 -KYHNVGLSKCEIKV 74

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 1e-10
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 24 TKLYISNLDYGVSNEDIK----ELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVA 79
            +YI+NL+  +  +++K     +FS  G +    +      + +G A V++   + A  
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATN 61

Query: 80 AVKRYNNVQLDGKPMKIE 97
          A++         KPM+I+
Sbjct: 62 ALRSMQGFPFYDKPMRIQ 79

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.6 bits (128), Expect = 1e-10
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 1/90 (1%)

Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR-SKGTAEVVYSRRADAVAAVK 82
            +L++ NL Y  S ED+++LFS  G L       D   +  KG A V +     AV A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 83  RYNNVQLDGKPMKIEIVGTNIATRTAAPAA 112
             +     G+ + +           + P++
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 1e-10
 Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIH-YDRSGRSKGTAEVVYSRRADAVAAVKR 83
          K+++  L    + ED+K  F + G +    +     + R +G   V +          + 
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 84 YNNVQLDGKPMKIE 97
           +  +++ K ++ +
Sbjct: 60 IHFHEINNKMVECK 73

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (128), Expect = 2e-10
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 14 AGRASAIETGTKLYISNLD-YGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYS 72
          +G+       ++++I NL+   V   D++ +FS+ G +   S+H        G A V Y 
Sbjct: 6  SGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYV 58

Query: 73 RRADAVAAVKRYNNVQLDGKPMKIEI 98
             +A AAV   +   + G+ + I +
Sbjct: 59 NERNARAAVAGEDGRMIAGQVLDINL 84

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 2e-10
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
           ++ + NL Y V+ + + ++FS+ G + +          ++  A + Y+    A  A   
Sbjct: 8  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLS 64

Query: 84 YNNVQLDGKPMKIEI 98
           +   +      + I
Sbjct: 65 LDGQNIYNACCTLRI 79

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 2e-10
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYD---------RSGRSKGTAEVVYSR 73
           + +Y+  L+  V+ +D+ + F + G +K                 +G+ KG A V Y  
Sbjct: 8  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 74 RADAVAAVKRYNNVQLDGKPMKIEI 98
             A AAV+ ++     G  +K+ +
Sbjct: 68 PPTAKAAVEWFDGKDFQGSKLKVSL 92

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.6 bits (125), Expect = 3e-10
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRAD 76
           S   T   L+I NL+   S  ++K   SE+      ++   R+G ++    V +    D
Sbjct: 7  GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66

Query: 77 AVAAVKRYNNVQLDGKPMKIE 97
             A+     +++ G  +K+E
Sbjct: 67 LEKAL-ELTGLKVFGNEIKLE 86

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 5e-10
 Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
            +YI       + +DIKE   + G +    +        KG+  VV+     A   V+ 
Sbjct: 7  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 66

Query: 84 YNNVQLDGKPMKIE 97
              +     + I 
Sbjct: 67 -PGQKYKETDLLIL 79

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 5e-10
 Identities = 16/74 (21%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRY-SIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          KL++  L +  + + ++++FS+ G +     +    + RS+G   V +    DA  A+  
Sbjct: 7  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 84 YNNVQLDGKPMKIE 97
           N   +DG+ ++++
Sbjct: 67 MNGKSVDGRQIRVD 80

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (124), Expect = 5e-10
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR-SKGTAEVVYSRRAD 76
          S +  G  ++I NL +    E + E+  + GDLK   +        SKG A   +  +  
Sbjct: 3  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 77 AVAAVKRYN------NVQLDGKPMKIEI 98
          A   +   +       ++LDG+ +K+++
Sbjct: 63 AQKCLAAASLEAEGGGLKLDGRQLKVDL 90

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 6e-10
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAV 78
          A   G  LY+   D  ++   ++  FS        +I        +  A V Y +   A 
Sbjct: 1  APRKGNTLYVYGED--MTPTLLRGAFS-----PFGNIIDLSMDPPRNCAFVTYEKMESAD 53

Query: 79 AAVKRYNNVQLDGKPMKIEI 98
           AV   N  Q++   +K+ I
Sbjct: 54 QAVAELNGTQVESVQLKVNI 73

>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 = 50.5 bits (120), Expect = 1e-09
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          KLYI NL   V+ +D+++LF +        +         G A V Y  +  A+ A++  
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETL 57

Query: 85 N-NVQLDGKPMKIE 97
          +  V+L GK M+++
Sbjct: 58 SGKVELHGKIMEVD 71

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 1e-09
 Identities = 12/76 (15%), Positives = 28/76 (36%)

Query: 22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAV 81
          T  K+++  +        +++ F + G ++   I  DR    K     V     D+V  +
Sbjct: 1  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 60

Query: 82 KRYNNVQLDGKPMKIE 97
                 ++G   ++ 
Sbjct: 61 VIQKYHTVNGHNCEVR 76

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 2e-09
 Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYS------IHYDRSGRSKGTAEVVYSRRADAV 78
          +LY+ N+ +G++ E + + F+    L   +      +   +  + K  A + +    +  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 79 AAVKRYNNVQLDGKPMKI 96
           A+  ++ +   G+ +KI
Sbjct: 63 QAM-AFDGIIFQGQSLKI 79

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 3e-09
 Identities = 27/111 (24%), Positives = 48/111 (43%), Gaps = 17/111 (15%)

Query: 21  ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSG-RSKGTAEVVYSRRADAVA 79
            T TK+++  L Y  ++  +++ F   GD++   +  DR   +S+G   V  + RA A  
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 80  AVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNGVPRGGQGRG 130
           A K  N + +DG+   +     N+A   A P +           + G   G
Sbjct: 68  ACKDPNPI-IDGRKANV-----NLAYLGAKPRS----------LQTGFAIG 102

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.7 bits (118), Expect = 3e-09
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 23 GTKLYISNLDYGVSNED-IKELFSEVGDL--KRYSIHYDRSGRSKGTAEVVYSRRADAVA 79
          G ++ I NL   + +E+ ++E F   G +              +   A +V+  +  A  
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 80 AVKRYNNVQLDGKPMKIEI 98
          A++  N   L  + + + +
Sbjct: 64 ALQ-MNRSLLGNREISVSL 81

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 4e-09
 Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 1/71 (1%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIH-YDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          LYI  L  G +++D+ +L    G +          + + KG   V +   + A  AV   
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 85 NNVQLDGKPMK 95
              +  +  K
Sbjct: 61 KASGVQAQMAK 71

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 49.5 bits (117), Expect = 1e-08
 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 5/102 (4%)

Query: 21  ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSG-RSKGTAEVVYSRRADAVA 79
           +    L ++ +   V    +++LF   G ++   I  DR   +S+G   V +   + A  
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 80  AVKRYNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNG 121
           A+   N   +  K +K+ +     A+    P      G+ NG
Sbjct: 100 AIAGLNGFNILNKRLKVALA----ASGHQRPGIAGAVGDGNG 137

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVA 79
          E    LY+ NL   V+  D+  LF+   + K   I +   +GR +G A + +  +  A  
Sbjct: 16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 80 AVKRYNNVQLDGKPMKIEI 98
          A+   N  +L GK + IE 
Sbjct: 76 ALHLVNGYKLYGKILVIEF 94

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 3e-08
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGR-SKGTAEVVYSRRADAVAAVKR 83
           +++ N+ Y  + E +K++FSEVG +  + + YDR     KG     Y  +  A++A++ 
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 84 YNNVQLDGKPMKIE 97
           N  +  G+ ++++
Sbjct: 70 LNGREFSGRALRVD 83

>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 = 47.4 bits (112), Expect = 3e-08
 Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 11/98 (11%)

Query: 25  KLYISNLDYGVSNEDIKELFSEVGDLKRYSI-HYDRSGRSKGTAEVVYSRRADAVAAVKR 83
             ++ NL Y V+ E IKE F  +               R KG     +      ++A+  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 84  YNNVQLDGKPMKIEIVGTNIATRTAAPAANVNFGNSNG 121
            N   L  K +++++         A  A + + G S+G
Sbjct: 76  LNEESLGNKRIRVDV---------ADQAQDKDSGPSSG 104

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 4e-08
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          + + + NL    + +++ +L  +      Y         +K TA V       A  A++ 
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR------NKRTAFVTLLNGEQAQNAIQM 59

Query: 84 YNNVQLDGKPMKIEI 98
          ++     GK + +++
Sbjct: 60 FHQYSFRGKDLIVQL 74

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.0 bits (108), Expect = 7e-08
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 25 KLYISNLDYGVSNEDI---KELFSEVGDLKRYSIHYDR----SGRSKGTAEVVYSRRADA 77
           +++  L   +++ ++    E F + G + +  I+       S     +A V Y R  DA
Sbjct: 10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 78 VAAVKRYNNVQLDGKPMKI 96
          + A++  NNV +DG+ +K 
Sbjct: 70 LRAIQCVNNVVVDGRTLKA 88

>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 = 45.4 bits (107), Expect = 1e-07
 Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T+L++  L    S   +   F      +  SI      +    A + Y     A AA  +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFD-----RFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72

Query: 84 YNNVQLDGKPMKIEI 98
               L G   ++ +
Sbjct: 73 MRGFPLGGPDRRLRV 87

>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 = 47.3 bits (111), Expect = 1e-07
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          KL+I  L +  ++E ++  F + G L     +    + RS+G   V Y+   +  AA+  
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 84 YNN 86
            +
Sbjct: 68 RPH 70

>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 = 44.7 bits (105), Expect = 2e-07
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 24  TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
             L++SN+   VS ED+K LFS  G + +    + +  +      +      +AV A+  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA---LIQMGSVEEAVQALID 67

Query: 84  YNNVQL-DGKPMKIEIVGTNI 103
            +N  L +   +++    + I
Sbjct: 68  LHNHDLGENHHLRVSFSKSTI 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.8 bits (105), Expect = 3e-07
 Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
          +G      +  ++ +S L    S +D+K+   E GD+    +  D          V Y R
Sbjct: 6  SGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG------MGMVEYLR 59

Query: 74 RADAVAAVKRYNNVQLDGKPMKIEIV 99
          + D   A+++ ++ +      +   +
Sbjct: 60 KEDMEYALRKLDDTKFRSHEGETSYI 85

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 5e-07
 Identities = 14/79 (17%), Positives = 25/79 (31%), Gaps = 10/79 (12%)

Query: 24 TKLYISNLDYGVSNE-----DIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAV 78
          + L     +  V +E       + LF        +        +S     + +S    A 
Sbjct: 6  SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPLSAA 60

Query: 79 AAVKRYNNVQLDGKPMKIE 97
           A  R +  +  GK MK+ 
Sbjct: 61 DARLRLHKTEFLGKEMKLY 79

>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 = 42.3 bits (99), Expect = 2e-06
 Identities = 11/75 (14%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          + +++      ++ ++++E FS+ GD+    I        +  A V ++    A +    
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF----RAFAFVTFADDQIAQSLCG- 60

Query: 84 YNNVQLDGKPMKIEI 98
            ++ + G  + I  
Sbjct: 61 -EDLIIKGISVHISN 74

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.4 bits (96), Expect = 2e-06
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 26  LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
           + I  L   V+N+++ +L S+      Y + Y    + KGTA V       A AA+  ++
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 86  NVQLDGKPMKIEIVGTN 102
             +L  + + +++  T+
Sbjct: 55  QSRLRERELSVQLQPTD 71

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 3e-06
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 24 TKLYISNLD-YGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK 82
          + L +SNL+   V+ + +  LF   GD++R  I +++    K  A V  +    A  A+ 
Sbjct: 3  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMS 58

Query: 83 RYNNVQLDGKPMKIEI 98
            N  +L GKP++I +
Sbjct: 59 HLNGHKLHGKPIRITL 74

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.5 bits (94), Expect = 7e-06
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 16 RASAIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR 74
          +   +ET   ++I +   G      + +L    G +  + I    +      A +  +  
Sbjct: 1  QKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN-----EAFIEMATT 55

Query: 75 ADAVAAVKRY--NNVQLDGKPMKIE 97
           DA AAV  Y      + GKP+++ 
Sbjct: 56 EDAQAAVDYYTTTPALVFGKPVRVH 80

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (95), Expect = 7e-06
 Identities = 12/77 (15%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVK 82
             +I+N+ + ++  D+ +    +   +         +G+  G A V +    DA  + +
Sbjct: 9  VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 83 RYNNVQLDGKPMKIEIV 99
            +  +L+G+   + +V
Sbjct: 69 L-HRKKLNGREAFVHVV 84

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.9 bits (95), Expect = 7e-06
 Identities = 11/85 (12%), Positives = 25/85 (29%), Gaps = 5/85 (5%)

Query: 14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
          +G    +     +++  L   V   D+ E   + G +    +   +       A V +  
Sbjct: 6  SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFEN 60

Query: 74 RADAVAAVKRYNNVQLDGKPMKIEI 98
             A   V    +V +     +   
Sbjct: 61 IDSAKECVTFAADVPVYIAGQQAFF 85

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.2 bits (93), Expect = 7e-06
 Identities = 10/74 (13%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
          T + + NL    +   + + F   G +    +        +  A + ++R   A+AA+ +
Sbjct: 1  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAITK 59

Query: 84 YNNVQLDGKPMKIE 97
           +   +    + + 
Sbjct: 60 THK-VVGQNEIIVS 72

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 11/73 (15%), Positives = 27/73 (36%), Gaps = 3/73 (4%)

Query: 28 ISNLDYGVSNEDIKELFSEVGDLKRYSIHYD---RSGRSKGTAEVVYSRRADAVAAVKRY 84
          + + +Y    ED+++  S+ G +K   I            G   V ++   D   A++  
Sbjct: 19 LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 85 NNVQLDGKPMKIE 97
             +   + +  +
Sbjct: 79 TGRKFANRVVVTK 91

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 1e-05
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 7/75 (9%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
           L+I  L   V+  ++  L           +      + K  A +  +    A+  V  Y
Sbjct: 10 VLHIRKLPGEVTETEVIALGL-----PFGKVTNILMLKGKNQAFLELATEEAAITMVNYY 64

Query: 85 --NNVQLDGKPMKIE 97
                L  +P+ I+
Sbjct: 65 SAVTPHLRNQPIYIQ 79

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.1 bits (90), Expect = 2e-05
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKR 83
            L+++NL    +   +  LF++    K   +  +R       A V ++    + AA + 
Sbjct: 9  QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEA 64

Query: 84 YNNVQLD-GKPMKIE 97
              ++     MKI 
Sbjct: 65 LQGFKITPTHAMKIT 79

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 6/72 (8%)

Query: 26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN 85
          +    L  GVS   +  +       K   +       +K  +   Y    ++  A    N
Sbjct: 23 VANGGLGNGVSRNQLLPVLE-----KCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLN 77

Query: 86 NVQL-DGKPMKI 96
            ++ D    KI
Sbjct: 78 GKEVVDDLGQKI 89

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (86), Expect = 8e-05
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY 84
          ++ +S L    S +D+K+        +             GT  V + R+ D   AV++ 
Sbjct: 2  RVVVSGLPPSGSWQDLKDHM------REAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKL 55

Query: 85 NNVQLDGKPMKIEIV 99
          +N +      +   +
Sbjct: 56 DNTKFRSHEGETAYI 70

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (82), Expect = 5e-04
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRAD 76
           S+  + T +   NL  G    +I+E FS  G L R             TA V +    +
Sbjct: 4  GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRV-----LLPEGGITAIVEFLEPLE 58

Query: 77 AVAAVKRYNNVQLDGKPMKIE 97
          A  A +     +    P+ +E
Sbjct: 59 ARKAFRHLAYSKFHHVPLYLE 79

>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 = 35.6 bits (81), Expect = 8e-04
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEV-VYSRRADAVAAVK 82
             +  +LD     ED+  LFS  G++K                 +    +  +A+   K
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAK 66

Query: 83 RYNNVQLDGKPMKIEI 98
            NN  L  +  ++  
Sbjct: 67 DANNGNLQLRNKEVTW 82

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (79), Expect = 0.001
 Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSR 73
          +G +    TG  +++  L Y  +  DI   FS +  ++ +       GR  G A+V ++ 
Sbjct: 6  SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE-IGPDGRVTGEADVEFAT 64

Query: 74 RADAVAAVKRYNNVQLDGKPMKIEI 98
            DAVAA+ + +   +  + +++ +
Sbjct: 65 HEDAVAAMAK-DKANMQHRYVELFL 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	184
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.89
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.88
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.88
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.85
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.84
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.84
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.84
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.83
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.83
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.82
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.82
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.82
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.81
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.81
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.8
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.8
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.8
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.8
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.79
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.79
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.78
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.78
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.78
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.78
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.77
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.77
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.76
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.67
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.47
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.08
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.94
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.79
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.7

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=3e-23  Score=140.24  Aligned_cols=87  Identities=25%  Similarity=0.361  Sum_probs=80.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .....+++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         3 ~~~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V   82 (99)
T d1whwa_           3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV   82 (99)
T ss_dssp             CCCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344567889999999999999999999999999999999988 8999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      .++..+..
T Consensus        83 ~~a~~~~~   90 (99)
T d1whwa_          83 LPSTIKKE   90 (99)
T ss_dssp             EECCCCST
T ss_pred             EECCCCCc
Confidence            99987544

>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=99.89  E-value=3.6e-23  Score=136.96  Aligned_cols=84  Identities=25%  Similarity=0.445  Sum_probs=78.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....+++|||+|||.++++++|+++|++||.|..|+|+.++ ++++++||||+|.+.++|++|+..||+..|.|+.|+|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34568899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      ++.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99864

>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=99.89  E-value=9.6e-23  Score=136.25  Aligned_cols=83  Identities=30%  Similarity=0.465  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ...+++|||+|||+++++++|+++|++||+|..|.|+.++ ++.++|||||+|.+.++|+.||+.||+..|.|++|+|++
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3568999999999999999999999999999999999998 889999999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            8643

>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=99.89  E-value=2.4e-23  Score=135.91  Aligned_cols=79  Identities=24%  Similarity=0.392  Sum_probs=75.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      +++|||+|||+++++++|+++|++||.|..|+|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|+++++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            5789999999999999999999999999999999987 889999999999999999999999999999999999999875

>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=99.89  E-value=4.5e-23  Score=137.89  Aligned_cols=86  Identities=27%  Similarity=0.401  Sum_probs=79.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      ...+..++|||+|||.++++++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         4 ~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   83 (93)
T d1x5ua1           4 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   83 (93)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344556899999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      .++.++.
T Consensus        84 ~~A~~~~   90 (93)
T d1x5ua1          84 NKASAHN   90 (93)
T ss_dssp             EETTTTS
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.89  E-value=1e-22  Score=132.91  Aligned_cols=79  Identities=25%  Similarity=0.455  Sum_probs=75.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .++|||+|||.++++++|+++|++||.|..|+|+.+. +++++|||||+|.+.++|++|++.||+..|.|+.|+|++++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4679999999999999999999999999999999987 789999999999999999999999999999999999999875

>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=99.89  E-value=8.2e-23  Score=138.85  Aligned_cols=84  Identities=23%  Similarity=0.372  Sum_probs=78.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +++++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|+.||+.||+..|.|+.|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999999988 8999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q 030010          100 GTNIA  104 (184)
Q Consensus       100 ~~~~~  104 (184)
                      +++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87553

>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=99.88  E-value=1.1e-22  Score=135.17  Aligned_cols=83  Identities=25%  Similarity=0.438  Sum_probs=78.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .++.++|||+|||.++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4467899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      ++++
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9864

>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=99.88  E-value=1.2e-22  Score=132.99  Aligned_cols=77  Identities=32%  Similarity=0.491  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKI   96 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V   96 (184)
                      .+++++|||+|||+.+|+++|+++|++||.|..|+|+.++ ++++++||||+|.+.++|++||+.||+..|.|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4567899999999999999999999999999999999998 7999999999999999999999999999999999987

>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=99.88  E-value=4.2e-22  Score=142.36  Aligned_cols=84  Identities=19%  Similarity=0.327  Sum_probs=78.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .+..++|||+|||+++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3445789999999999999999999999999999999998 889999999999999999999999999999999999999


Q ss_pred             eeCCC
Q 030010           99 VGTNI  103 (184)
Q Consensus        99 ~~~~~  103 (184)
                      +....
T Consensus       119 a~~~~  123 (139)
T d1u6fa1         119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            87544

>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=99.88  E-value=1.3e-22  Score=131.38  Aligned_cols=76  Identities=61%  Similarity=1.025  Sum_probs=73.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      +|||+|||+++++++|+++|++||.|..|+|..+++++++|||||+|.+.++|++||+.||+..|.|++|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.88  E-value=9.7e-23  Score=134.03  Aligned_cols=80  Identities=28%  Similarity=0.402  Sum_probs=76.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      ++|||+|||+++++++|+++|++||+|..|+|+.++ ++++++||||+|.++++|+.|++.||+..|.|++|+|+++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            589999999999999999999999999999999998 8999999999999999999999999999999999999999754


Q ss_pred             C
Q 030010          103 I  103 (184)
Q Consensus       103 ~  103 (184)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.6e-22  Score=131.46  Aligned_cols=76  Identities=30%  Similarity=0.391  Sum_probs=73.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      +|||+|||+.+|+++|+++|++||+|..|+|+.++ ++++++||||+|.++++|+.||+.||+..|.|++|+|.+++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999998 89999999999999999999999999999999999999985

>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=99.88  E-value=7.7e-23  Score=135.61  Aligned_cols=81  Identities=25%  Similarity=0.403  Sum_probs=77.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||+++++++|+++|++||+|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|++++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46899999999999999999999999999999999988 79999999999999999999999999999999999999997


Q ss_pred             CC
Q 030010          101 TN  102 (184)
Q Consensus       101 ~~  102 (184)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.87  E-value=3.4e-22  Score=133.80  Aligned_cols=85  Identities=24%  Similarity=0.443  Sum_probs=78.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC--CCCcceEEEEEecCHHHHHHHHHHh-CCCccCCceEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR--SGRSKGTAEVVYSRRADAVAAVKRY-NNVQLDGKPMKI   96 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~--~~~~~g~afV~F~~~e~a~~Ai~~l-~g~~~~g~~i~V   96 (184)
                      ..++++|||+|||+++++++|+++|++||.|..|+|+.+.  +++++|||||+|.+.++|++||+.| |+..|.|++|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            4567889999999999999999999999999999998875  7899999999999999999999998 899999999999


Q ss_pred             EEeeCCCC
Q 030010           97 EIVGTNIA  104 (184)
Q Consensus        97 ~~~~~~~~  104 (184)
                      +++.....
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987543

>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=99.87  E-value=5.8e-22  Score=130.21  Aligned_cols=79  Identities=29%  Similarity=0.604  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMKIE   97 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V~   97 (184)
                      ...++|||+|||+++++++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|++||+.||+..+.+  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            456789999999999999999999999999999999998 89999999999999999999999999999876  889999


Q ss_pred             Ee
Q 030010           98 IV   99 (184)
Q Consensus        98 ~~   99 (184)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.4e-22  Score=130.84  Aligned_cols=79  Identities=25%  Similarity=0.505  Sum_probs=73.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEEEE
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMKIE   97 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V~   97 (184)
                      ..+++|||+|||+++++++|+++|++||+|..|+|+.++ ++++++||||+|.+.++|++|++.||+..+.|  ++|+|.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            456889999999999999999999999999999999998 89999999999999999999999999999987  568888


Q ss_pred             Ee
Q 030010           98 IV   99 (184)
Q Consensus        98 ~~   99 (184)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.87  E-value=5.6e-22  Score=131.59  Aligned_cols=83  Identities=23%  Similarity=0.480  Sum_probs=77.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ...+|||+|||+++++++|+++|++||.|..+.++.+. ++.++|||||+|.++++|+.||+.||+..|.|+.|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            46789999999999999999999999999999988887 88999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 030010          101 TNIA  104 (184)
Q Consensus       101 ~~~~  104 (184)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.87  E-value=9.5e-22  Score=133.73  Aligned_cols=81  Identities=27%  Similarity=0.459  Sum_probs=75.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||+.+|+ .|.|+.|+|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            45789999999999999999999999999999999998 899999999999999999999998775 7999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            644

>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=99.86  E-value=1.9e-21  Score=129.80  Aligned_cols=87  Identities=21%  Similarity=0.447  Sum_probs=78.5

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ........++|||+|||+++++++|+++|++||+|..|.|+.++.+ +++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus         4 ~~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   82 (93)
T d2cq3a1           4 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIE   82 (93)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3445556788999999999999999999999999999999988743 589999999999999999999999999999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |++++++.
T Consensus        83 V~~A~~r~   90 (93)
T d2cq3a1          83 VNNATARV   90 (93)
T ss_dssp             EEECCSSC
T ss_pred             EEecCcCC
Confidence            99998754

>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=99.86  E-value=3.5e-22  Score=130.08  Aligned_cols=78  Identities=14%  Similarity=0.248  Sum_probs=69.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+. ++++++||||+|.+.++|++||+.||+..|.|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            799999999999999999999999999888777766 889999999999999999999999999999999999999875

>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=99.86  E-value=1.7e-21  Score=129.29  Aligned_cols=83  Identities=22%  Similarity=0.386  Sum_probs=75.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|++||+.  .+.|+|+.|.|.
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEE
Confidence            34567899999999999999999999999999999999998 899999999999999999999984  458999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      ++.++.
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            987643

>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=99.86  E-value=2.8e-22  Score=129.45  Aligned_cols=75  Identities=23%  Similarity=0.444  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      |+|||+|||+++++++|+++|++||.|..++|+.++ +++++|||||+|.+.++|++||+ ++++.|+|+.|+|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999998 89999999999999999999996 7999999999999876

>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=99.85  E-value=2.3e-21  Score=130.35  Aligned_cols=87  Identities=24%  Similarity=0.436  Sum_probs=78.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhC------CCcc
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYN------NVQL   89 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~------g~~~   89 (184)
                      |+....+++|||+|||+++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++||+.||      +..|
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~   81 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   81 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE
Confidence            4556678999999999999999999999999999999999888 78899999999999999999999887      5678


Q ss_pred             CCceEEEEEeeCCC
Q 030010           90 DGKPMKIEIVGTNI  103 (184)
Q Consensus        90 ~g~~i~V~~~~~~~  103 (184)
                      .|+.|+|+++.++.
T Consensus        82 ~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          82 DGRQLKVDLAVTRD   95 (98)
T ss_dssp             SSCEEEEECCCCCC
T ss_pred             CCEEEEEEECCCCC
Confidence            89999999987643

>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=99.85  E-value=3.6e-21  Score=127.69  Aligned_cols=82  Identities=26%  Similarity=0.332  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .+.++|||+|||.++++++|+++|++||+|..|+|+.++.. .++||||+|.+.++|++|++.||+..|.|+.|+|.+++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            44679999999999999999999999999999999988733 36799999999999999999999999999999999997


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.85  E-value=1.3e-21  Score=128.42  Aligned_cols=77  Identities=29%  Similarity=0.506  Sum_probs=71.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CC---CcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SG---RSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~---~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      |||+|||+++++++|+++|++||.|..|.|+.++ ++   .++|||||+|.+.++|++||+.||+..|.|+.|+|+++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999998876 33   4689999999999999999999999999999999999864


Q ss_pred             C
Q 030010          102 N  102 (184)
Q Consensus       102 ~  102 (184)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.85  E-value=3.4e-22  Score=136.12  Aligned_cols=82  Identities=24%  Similarity=0.588  Sum_probs=76.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|+++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999988 89999999999999999999999999999999999999987


Q ss_pred             CCC
Q 030010          101 TNI  103 (184)
Q Consensus       101 ~~~  103 (184)
                      +..
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.85  E-value=3.2e-21  Score=126.37  Aligned_cols=78  Identities=23%  Similarity=0.371  Sum_probs=73.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ...+|||+|||+++++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+ ++++.|.|+.|+|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34789999999999999999999999999999999998 89999999999999999999997 68999999999998874

>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=99.85  E-value=1.2e-21  Score=128.04  Aligned_cols=78  Identities=24%  Similarity=0.339  Sum_probs=72.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEE-EEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCC
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRY-SIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNI  103 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v-~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~  103 (184)
                      |||+|||+++++++|+++|++||.|..+ .|+.++ +++++|||||+|.+.++|++||+.||+..|.|++|+|+++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998654 678777 88999999999999999999999999999999999999987643

>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=99.85  E-value=1.4e-21  Score=125.40  Aligned_cols=73  Identities=23%  Similarity=0.508  Sum_probs=69.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      +|||+|||++++|++|+++|++||+|..|.|+.++ +++++|||||+|.+.++|++||+ +++..|.|+.|.|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            59999999999999999999999999999999988 89999999999999999999996 799999999999864

>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=99.84  E-value=3.3e-21  Score=130.31  Aligned_cols=88  Identities=24%  Similarity=0.472  Sum_probs=78.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeE--------EEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLK--------RYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNV   87 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~--------~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~   87 (184)
                      |......++|||+|||+.+++++|+++|++||.|.        .+.+..++ ++++++||||+|.+.++|.+||+.||+.
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            44556788999999999999999999999999874        45666776 7899999999999999999999999999


Q ss_pred             ccCCceEEEEEeeCCCC
Q 030010           88 QLDGKPMKIEIVGTNIA  104 (184)
Q Consensus        88 ~~~g~~i~V~~~~~~~~  104 (184)
                      .|.|+.|+|+++++..+
T Consensus        82 ~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          82 DFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             EECCEEEEEEEcCCCCC
Confidence            99999999999986443

>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=99.84  E-value=9.2e-22  Score=133.36  Aligned_cols=78  Identities=26%  Similarity=0.401  Sum_probs=74.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .++|||+|||+++++++|+++|+.||.|..|.|+.++ +++++|||||+|.+.++|++||+ ||+..|.|+.|+|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            5789999999999999999999999999999999998 89999999999999999999995 999999999999998764

>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=99.84  E-value=1e-20  Score=126.62  Aligned_cols=84  Identities=21%  Similarity=0.353  Sum_probs=75.2

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      +.+..++.++|||+|||+++++++|+++|++||.|..+.+..+  ...++||||+|.+.++|++||+.||+..|.+++|+
T Consensus         7 ~~p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~   84 (95)
T d1x4aa1           7 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   84 (95)
T ss_dssp             SCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4455677889999999999999999999999999998887543  44678999999999999999999999999999999


Q ss_pred             EEEeeC
Q 030010           96 IEIVGT  101 (184)
Q Consensus        96 V~~~~~  101 (184)
                      |++++.
T Consensus        85 V~~a~~   90 (95)
T d1x4aa1          85 VEFPRS   90 (95)
T ss_dssp             EECCCC
T ss_pred             EEeccC
Confidence            999874

>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=99.84  E-value=2.1e-21  Score=128.56  Aligned_cols=80  Identities=21%  Similarity=0.361  Sum_probs=73.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      ..+|||+|||+++++++|+++|++||.|..++|+.++. .+++||||+|.+.++|++||+.||+..|.|+.|+|++++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            45799999999999999999999999999999988763 36789999999999999999999999999999999999865


Q ss_pred             C
Q 030010          103 I  103 (184)
Q Consensus       103 ~  103 (184)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.84  E-value=1.1e-20  Score=122.20  Aligned_cols=76  Identities=17%  Similarity=0.357  Sum_probs=71.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      .++|||+|||+++|+++|+++|++||.|..+.+..++ +++++|||||+|.+++++++|++ +++..|.|+.|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4789999999999999999999999999999999998 88999999999999999999995 8999999999999875

>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=99.84  E-value=9.3e-21  Score=128.83  Aligned_cols=86  Identities=19%  Similarity=0.328  Sum_probs=75.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC--CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR--SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~--~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ..+..+.++|||+|||+.+++++|+++|++|| |..+.++.+.  ++++++||||+|.+.++|++|+ .||+..|.++.|
T Consensus         9 ~~p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l   86 (104)
T d1wi8a_           9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEE
Confidence            34456779999999999999999999999998 7778777765  6789999999999999998777 599999999999


Q ss_pred             EEEEeeCCCC
Q 030010           95 KIEIVGTNIA  104 (184)
Q Consensus        95 ~V~~~~~~~~  104 (184)
                      +|.++.+...
T Consensus        87 ~V~~a~~~~~   96 (104)
T d1wi8a_          87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999876443

>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=99.84  E-value=4e-21  Score=130.59  Aligned_cols=80  Identities=24%  Similarity=0.352  Sum_probs=74.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .++|||+|||+++++++|+++|++||.|..+.|..++ ++.++|||||+|.+.++|++||+ +++..|.|+.|.|.++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            4799999999999999999999999999999999998 78999999999999999999995 799999999999999876


Q ss_pred             CC
Q 030010          102 NI  103 (184)
Q Consensus       102 ~~  103 (184)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.84  E-value=1.3e-20  Score=130.14  Aligned_cols=80  Identities=24%  Similarity=0.402  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      .+.+++|||+|||..+++++|+++|++||.|..|.+..+  +.++|||||+|.+.++|..||+.||+..|.|+.|+|.++
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345789999999999999999999999999999988754  456899999999999999999999999999999999998


Q ss_pred             eC
Q 030010          100 GT  101 (184)
Q Consensus       100 ~~  101 (184)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            65

>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=99.84  E-value=3.9e-21  Score=126.51  Aligned_cols=80  Identities=18%  Similarity=0.328  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHHhhCCCeEEEEEEeCC--CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           22 TGTKLYISNLDYGVS-NEDIKELFSEVGDLKRYSIHYDR--SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        22 ~~~~l~V~nLp~~~t-e~~L~~~f~~~G~i~~v~i~~~~--~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++|||+|||++++ +++|+++|++||.|..|+|..+.  +++++|||||+|.+.++|++||+ ||+..|.|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            578999999999875 66799999999999999987654  78899999999999999999995 999999999999999


Q ss_pred             eeCC
Q 030010           99 VGTN  102 (184)
Q Consensus        99 ~~~~  102 (184)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>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=99.84  E-value=8.3e-21  Score=128.52  Aligned_cols=81  Identities=21%  Similarity=0.322  Sum_probs=75.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ...++|||+|||+++++++|+++|++||.|..+.+..+.++.+++||||+|.+.++|++||+.|||..|.|+++.|..++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            34689999999999999999999999999999999988888999999999999999999999999999999998886654


Q ss_pred             C
Q 030010          101 T  101 (184)
Q Consensus       101 ~  101 (184)
                      +
T Consensus        96 P   96 (101)
T d1x5oa1          96 P   96 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.83  E-value=2.2e-21  Score=124.48  Aligned_cols=74  Identities=14%  Similarity=0.340  Sum_probs=69.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +|||+|||+++|+++|+++|++||+|..|.|+.++ +++++|||||+|.+.++|++||+ .+++.|.|+.|.|.+|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999998 89999999999999999999996 4778999999998764

>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=99.83  E-value=1.8e-20  Score=127.04  Aligned_cols=88  Identities=25%  Similarity=0.379  Sum_probs=77.9

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP   93 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~   93 (184)
                      ++.......+++|||+|||+++|+++|+++|..|+ |..|.++.+.++++++||||+|.+.++|++|++ +|+..|.|+.
T Consensus         6 ~~~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~   83 (102)
T d1weza_           6 SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             CCSSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC
T ss_pred             CCCCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            34455666778999999999999999999999997 457888888888999999999999999999986 8999999999


Q ss_pred             EEEEEeeCCC
Q 030010           94 MKIEIVGTNI  103 (184)
Q Consensus        94 i~V~~~~~~~  103 (184)
                      |+|.++....
T Consensus        84 I~V~~s~~~~   93 (102)
T d1weza_          84 VELFLNSTAG   93 (102)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEcCCCC
Confidence            9999987644

>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=99.83  E-value=6e-21  Score=122.21  Aligned_cols=74  Identities=16%  Similarity=0.361  Sum_probs=70.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           25 KLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        25 ~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +|||+|||+++|+++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++ +|+..|.|++|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999998888 78999999999999999999996 9999999999999875

>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=99.83  E-value=2.1e-21  Score=131.60  Aligned_cols=85  Identities=27%  Similarity=0.374  Sum_probs=78.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      +.+++++|||+|||..+++++|+++|++||.|..+.++.+. ++++++||||+|.+.++|+.||+.||+..|.|+.|+|+
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34568999999999999999999999999999988888777 88999999999999999999999999999999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      +++++.
T Consensus        94 ~ak~k~   99 (102)
T d2cpxa1          94 FGKNKK   99 (102)
T ss_dssp             ECCCCS
T ss_pred             eCCCcc
Confidence            998754

>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=99.83  E-value=2.2e-20  Score=125.76  Aligned_cols=80  Identities=26%  Similarity=0.451  Sum_probs=71.8

Q ss_pred             CCCCCCCCCEEEEcCCC-CCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           16 RASAIETGTKLYISNLD-YGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp-~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      .+.+....++|||+||| ..+++++|+++|++||.|..|.|.       ++||||+|.+.++|++||+.||+..|.|++|
T Consensus         8 ~~~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (98)
T d1wf2a_           8 KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVL   80 (98)
T ss_dssp             CCCCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34556667889999996 578899999999999999999984       7899999999999999999999999999999


Q ss_pred             EEEEeeCC
Q 030010           95 KIEIVGTN  102 (184)
Q Consensus        95 ~V~~~~~~  102 (184)
                      +|+++.++
T Consensus        81 ~V~~a~~~   88 (98)
T d1wf2a_          81 DINLAAEP   88 (98)
T ss_dssp             EEEETTSC
T ss_pred             EEEECCCC
Confidence            99998753

>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=99.83  E-value=3e-20  Score=125.13  Aligned_cols=83  Identities=17%  Similarity=0.255  Sum_probs=74.9

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .|+.....++|||+|||+.+++++|+++|++||+|+.|+|..      ++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus         8 gp~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_           8 GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             CCCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            455566788999999999999999999999999999999863      57999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q 030010           96 IEIVGTNIA  104 (184)
Q Consensus        96 V~~~~~~~~  104 (184)
                      |.+++....
T Consensus        82 v~~~~~~~~   90 (98)
T d1wg4a_          82 TSYIRVYPE   90 (98)
T ss_dssp             EEEEEEECC
T ss_pred             EEEEecCCC
Confidence            999976543

>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=99.83  E-value=5.8e-22  Score=131.89  Aligned_cols=83  Identities=22%  Similarity=0.239  Sum_probs=75.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ......++|||+|||+.+++++|+++|++||.|..+.|+.+.+++++|||||+|.+.++|++||+ ||+..|.|+.|+|+
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            34455779999999999999999999999999998888766689999999999999999999996 99999999999999


Q ss_pred             EeeC
Q 030010           98 IVGT  101 (184)
Q Consensus        98 ~~~~  101 (184)
                      +++.
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9875

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=1.7e-20  Score=123.23  Aligned_cols=79  Identities=23%  Similarity=0.381  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +..+.|||+|||+++++++|+++|+.|+.|.. +.+..+.+++++|+|||+|.+.++|++||+.||+..|.+++|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999865 56777779999999999999999999999999999999999999874

>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=99.82  E-value=4.2e-20  Score=121.21  Aligned_cols=77  Identities=18%  Similarity=0.227  Sum_probs=73.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      .++|||+|||.++|+++|+++|+.||+|..|.|..+++++++|||||+|.+.++|++||+ +++..|.|+.|.|.++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            578999999999999999999999999999999988899999999999999999999995 79999999999999864

>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=99.82  E-value=3.4e-20  Score=124.34  Aligned_cols=76  Identities=18%  Similarity=0.330  Sum_probs=71.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ..++|||+|||..+++++|+++|++||.|..|+|+.+     ++||||+|.+.++|++||..||+..|.|+.|+|+|+++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4678999999999999999999999999999999865     67999999999999999999999999999999999875


Q ss_pred             C
Q 030010          102 N  102 (184)
Q Consensus       102 ~  102 (184)
                      .
T Consensus        92 ~   92 (96)
T d1x4ga1          92 S   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.82  E-value=1.1e-19  Score=123.59  Aligned_cols=90  Identities=21%  Similarity=0.280  Sum_probs=76.4

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEE-EEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCc
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRY-SIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGK   92 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v-~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~   92 (184)
                      .+..+......+|||+|||+++||++|+++|..+|.|..+ .++.+.+++++|||||+|.++++|++|++ +|+..|.++
T Consensus         6 ~~~~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR   84 (104)
T d1wg5a_           6 SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHR   84 (104)
T ss_dssp             CCCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSS
T ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcce
Confidence            3344555567789999999999999999999999988764 44444488999999999999999999995 899999999


Q ss_pred             eEEEEEeeCCCC
Q 030010           93 PMKIEIVGTNIA  104 (184)
Q Consensus        93 ~i~V~~~~~~~~  104 (184)
                      .|+|.++.+...
T Consensus        85 ~i~V~~~~~~~~   96 (104)
T d1wg5a_          85 YIEIFKSSRAEV   96 (104)
T ss_dssp             CCEEEEECTTTS
T ss_pred             EEEEEECCHHHh
Confidence            999999986543

>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=99.82  E-value=6.7e-20  Score=119.64  Aligned_cols=78  Identities=18%  Similarity=0.248  Sum_probs=70.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CceEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD-GKPMKIE   97 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~-g~~i~V~   97 (184)
                      ..+|+++|||+|||.++++++|+++|++||.|..|+++.++    ++||||+|.+.++|++|++.||+..|. ++.|+|+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            34467899999999999999999999999999999997543    579999999999999999999998885 6899999


Q ss_pred             Eee
Q 030010           98 IVG  100 (184)
Q Consensus        98 ~~~  100 (184)
                      |++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2.7e-20  Score=127.79  Aligned_cols=81  Identities=22%  Similarity=0.255  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      .....++|||+|||+.+++++|+++|++||+|..|.|.     ..++||||+|.+.++|++||+.||+..|.|++|.|++
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~   80 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEE
Confidence            33456899999999999999999999999999999874     3467999999999999999999999999999999999


Q ss_pred             eeCCCC
Q 030010           99 VGTNIA  104 (184)
Q Consensus        99 ~~~~~~  104 (184)
                      +.....
T Consensus        81 a~~~~~   86 (111)
T d1whxa_          81 APIGVF   86 (111)
T ss_dssp             EETTTT
T ss_pred             CCCCcc
Confidence            976543

>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=99.81  E-value=7.1e-20  Score=120.37  Aligned_cols=77  Identities=25%  Similarity=0.424  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ..++|||+|||.++++++|+++|++||+|..|++..+     ++||||+|.+.++|++|++.||+..|.|+.|+|+++..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4578999999999999999999999999999999855     56999999999999999999999999999999999876


Q ss_pred             CC
Q 030010          102 NI  103 (184)
Q Consensus       102 ~~  103 (184)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            43

>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=99.81  E-value=6.2e-20  Score=122.99  Aligned_cols=83  Identities=19%  Similarity=0.263  Sum_probs=74.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhhCCC-eEEEEEEeCC--CCCcceEEEEEecCHHHHHHHHHHhCC--CccCCceEEEE
Q 030010           23 GTKLYISNLDYGVSNEDIKELFSEVGD-LKRYSIHYDR--SGRSKGTAEVVYSRRADAVAAVKRYNN--VQLDGKPMKIE   97 (184)
Q Consensus        23 ~~~l~V~nLp~~~te~~L~~~f~~~G~-i~~v~i~~~~--~~~~~g~afV~F~~~e~a~~Ai~~l~g--~~~~g~~i~V~   97 (184)
                      +|+|||+|||.++++++|+++|++||+ |..|.|+.+.  +++++|||||+|.++++|..||+.|++  ..+.++.|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 8999998875  578999999999999999999999875  55679999999


Q ss_pred             EeeCCCCC
Q 030010           98 IVGTNIAT  105 (184)
Q Consensus        98 ~~~~~~~~  105 (184)
                      ++++...+
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99875544

>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=99.80  E-value=2.2e-20  Score=123.07  Aligned_cols=74  Identities=22%  Similarity=0.344  Sum_probs=67.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTNI  103 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~~  103 (184)
                      ++|||+|||+++++++|+++|++||.|..++|..      .|||||+|.+.++|++||+.||+..|.|+.|+|.+++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            4699999999999999999999999999999864      3799999999999999999999999999999998876543

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.7e-19  Score=118.96  Aligned_cols=79  Identities=23%  Similarity=0.343  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQL-DGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~-~g~~i~V~~~   99 (184)
                      .|+++|||+|||+.+++++|+++|++||.|..+.+...+   .++||||+|.+.++|.+|+..||+..| +|+.|+|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS---STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec---ccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            457899999999999999999999999999888776443   467999999999999999999999888 5899999998


Q ss_pred             eCC
Q 030010          100 GTN  102 (184)
Q Consensus       100 ~~~  102 (184)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.80  E-value=1.6e-19  Score=123.44  Aligned_cols=77  Identities=29%  Similarity=0.430  Sum_probs=70.5

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           23 GTKLYISNLDY-GVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        23 ~~~l~V~nLp~-~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      +++|||+|||+ .+++++|+++|++||.|..|.|+.++    +|||||+|.+.++|++||+.||+..|.|+.|+|++++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            57999999954 69999999999999999999998764    67999999999999999999999999999999999875


Q ss_pred             CC
Q 030010          102 NI  103 (184)
Q Consensus       102 ~~  103 (184)
                      ..
T Consensus        78 ~~   79 (109)
T d2adca1          78 QN   79 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.80  E-value=1.3e-19  Score=117.25  Aligned_cols=75  Identities=24%  Similarity=0.387  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..+++|||+||+  +|+++|+++|++||.|..|.+..+     ++||||+|.+.++|++||+.||+..|.|+.|+|++++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            457899999996  899999999999999999998744     5699999999999999999999999999999999997


Q ss_pred             CC
Q 030010          101 TN  102 (184)
Q Consensus       101 ~~  102 (184)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.80  E-value=7.1e-20  Score=122.73  Aligned_cols=82  Identities=22%  Similarity=0.465  Sum_probs=72.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ....+.++|||+|||+++++++|+++|++||.|..+..    ++++++||||+|.+.++|++|++.||+..|.|+.|+|+
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34455789999999999999999999999998765542    56789999999999999999999999999999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      ++.++.
T Consensus        87 ~a~~k~   92 (96)
T d1fjca_          87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EeCCCC
Confidence            988643

>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=99.80  E-value=3e-19  Score=117.18  Aligned_cols=79  Identities=28%  Similarity=0.352  Sum_probs=70.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ....++|||+|||+++++++|+++|++||.|..+.+..     +++||||+|.+.++|.+||..||+..|.|+.|+|+++
T Consensus         5 ~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           5 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             ccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            34567999999999999999999999999988777753     4679999999999999999999999999999999998


Q ss_pred             eCCC
Q 030010          100 GTNI  103 (184)
Q Consensus       100 ~~~~  103 (184)
                      ++..
T Consensus        80 kP~~   83 (86)
T d2cpda1          80 KPVD   83 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7543

>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=99.79  E-value=2.9e-20  Score=118.14  Aligned_cols=70  Identities=23%  Similarity=0.350  Sum_probs=66.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      |||+|||+++++++|+++|++||.|..+++..++ ++.+++||||+|.+.++|++||+.||+..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            7999999999999999999999999999999988 889999999999999999999999999999998764

>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=99.79  E-value=2.9e-19  Score=114.47  Aligned_cols=74  Identities=14%  Similarity=0.216  Sum_probs=68.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ++|||+|||+++++++|+++|++||.|..|.+..++.+. ++||||+|.++++|++|+ .+|+..|.|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            589999999999999999999999999999999888544 469999999999999999 58999999999999865

>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=99.79  E-value=9.3e-20  Score=120.53  Aligned_cols=76  Identities=24%  Similarity=0.450  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHHhhCCCeEEEEEEeCC-CC---CcceEEEEEecCHHHHHHHHHHhCCCccCCceE
Q 030010           22 TGTKLYISNLDYGVSNEDI---KELFSEVGDLKRYSIHYDR-SG---RSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPM   94 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L---~~~f~~~G~i~~v~i~~~~-~~---~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i   94 (184)
                      ...+|||+|||+.+++++|   +++|++||+|..|.|+.++ ++   .+.+||||+|.+.++|++||+.||+..|.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3567999999999999999   7789999999999999887 43   345999999999999999999999999999999


Q ss_pred             EEE
Q 030010           95 KIE   97 (184)
Q Consensus        95 ~V~   97 (184)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.79  E-value=5e-19  Score=118.76  Aligned_cols=78  Identities=17%  Similarity=0.299  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--ceEEEE
Q 030010           20 IETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG--KPMKIE   97 (184)
Q Consensus        20 ~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g--~~i~V~   97 (184)
                      ..++++|||+|||+++++++|+++|++||.|..|++..+     ++||||+|.+.++|++|++.||+..|.+  ++|+|+
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            346789999999999999999999999999999998754     5699999999999999999999999986  589999


Q ss_pred             EeeCC
Q 030010           98 IVGTN  102 (184)
Q Consensus        98 ~~~~~  102 (184)
                      ++++.
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            98753

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.9e-19  Score=117.90  Aligned_cols=76  Identities=20%  Similarity=0.337  Sum_probs=66.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      .+++|||+|||+.+++++|+++|++|| +..+.+.     +.++||||+|.+.++|++||+.||+..|.|++|+|++++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            467899999999999999999999999 3333332     4578999999999999999999999999999999999975


Q ss_pred             CC
Q 030010          102 NI  103 (184)
Q Consensus       102 ~~  103 (184)
                      ..
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.78  E-value=1e-19  Score=117.99  Aligned_cols=75  Identities=27%  Similarity=0.369  Sum_probs=67.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCCceEEEEEeeCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNV-QLDGKPMKIEIVGTN  102 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~-~~~g~~i~V~~~~~~  102 (184)
                      ++|||+|||.++++++|+++|++||.|..+.+..     .++||||+|.+.++|++||+.||+. .|.|++|+|+++.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            4799999999999999999999999987766654     3679999999999999999999985 699999999999864


Q ss_pred             C
Q 030010          103 I  103 (184)
Q Consensus       103 ~  103 (184)
                      .
T Consensus        77 ~   77 (80)
T d2cqha1          77 K   77 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.3e-19  Score=120.29  Aligned_cols=80  Identities=25%  Similarity=0.484  Sum_probs=71.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           22 TGTKLYISNLDYGVSNEDIKE----LFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~----~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      |+++|||+|||+.+++++|++    +|++||+|..|.+.  +++++++||||+|.+.++|++|++.||+..|.|+.|+|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~--~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECC--HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEe--eeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            578999999999999998864    58999999988764  355678999999999999999999999999999999999


Q ss_pred             EeeCCC
Q 030010           98 IVGTNI  103 (184)
Q Consensus        98 ~~~~~~  103 (184)
                      +++++.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            998654

>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=99.78  E-value=5.8e-19  Score=120.65  Aligned_cols=82  Identities=15%  Similarity=0.190  Sum_probs=72.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC--CceEEE
Q 030010           19 AIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD--GKPMKI   96 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~--g~~i~V   96 (184)
                      ...+..+|||+|||+.+|+++|+++|++||.|..|.|..++   .++||||+|.+.++|+.||+.||+..|.  ++.|+|
T Consensus         3 ~~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           3 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            34567889999999999999999999999999999998764   4789999999999999999999999884  678888


Q ss_pred             EEeeCCC
Q 030010           97 EIVGTNI  103 (184)
Q Consensus        97 ~~~~~~~  103 (184)
                      .+++...
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            8887543

>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=99.77  E-value=4e-18  Score=115.68  Aligned_cols=83  Identities=14%  Similarity=0.094  Sum_probs=72.9

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCce
Q 030010           16 RASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY--NNVQLDGKP   93 (184)
Q Consensus        16 ~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l--~g~~~~g~~   93 (184)
                      ......++.+|||+|||..++|++|.++|++||.|..|.+..+     +++|||+|.+.++|++||+.|  +...+.+++
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~   82 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEE
Confidence            3455667999999999999999999999999999999998744     569999999999999999987  457788999


Q ss_pred             EEEEEeeCCC
Q 030010           94 MKIEIVGTNI  103 (184)
Q Consensus        94 i~V~~~~~~~  103 (184)
                      |+|.+++...
T Consensus        83 l~v~~s~~~~   92 (104)
T d1wexa_          83 AFFNYSTSKR   92 (104)
T ss_dssp             CEEEECSSSS
T ss_pred             EEEEEcCCCc
Confidence            9999997643

>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=99.77  E-value=2.8e-19  Score=123.09  Aligned_cols=88  Identities=18%  Similarity=0.339  Sum_probs=75.9

Q ss_pred             CCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEE-EEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           13 QAGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRY-SIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        13 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v-~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      ......+....++|||+|||+.+|+++|.++|+.||.|..+ .+..+.++.++|||||+|.+.++|++|++ ||+..|.+
T Consensus         8 ~~~~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~g   86 (112)
T d1wela1           8 RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN   86 (112)
T ss_dssp             CCCCSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT
T ss_pred             CCCCCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCC
Confidence            33445566678899999999999999999999999988654 44555599999999999999999999995 89999999


Q ss_pred             ceEEEEEeeC
Q 030010           92 KPMKIEIVGT  101 (184)
Q Consensus        92 ~~i~V~~~~~  101 (184)
                      +.|.|..+..
T Consensus        87 R~i~V~~~~~   96 (112)
T d1wela1          87 RFIQVHPITK   96 (112)
T ss_dssp             SCBEEEEECH
T ss_pred             EEEEEEEcCh
Confidence            9999998764

>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=99.77  E-value=1.8e-19  Score=118.81  Aligned_cols=78  Identities=14%  Similarity=0.244  Sum_probs=68.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      ..+++|||+|||+.+++++|+++|++||.|..|++..    .+++||||+|.+.++|++||.  +++.|.|++|+|.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            4578999999999999999999999999999987643    357899999999999999985  7889999999999987


Q ss_pred             CCCC
Q 030010          101 TNIA  104 (184)
Q Consensus       101 ~~~~  104 (184)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6443

>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=99.77  E-value=4.4e-19  Score=120.24  Aligned_cols=81  Identities=16%  Similarity=0.302  Sum_probs=72.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEE-EEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           21 ETGTKLYISNLDYGVSNEDIKELFSEVGDLKR-YSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~-v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      ....+|||+|||+++++++|+++|..||.|.. +.+..+.+++++|||||+|.+.++|++||+ +|+..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            44678999999999999999999999998876 555555699999999999999999999995 8999999999999987


Q ss_pred             eCC
Q 030010          100 GTN  102 (184)
Q Consensus       100 ~~~  102 (184)
                      ...
T Consensus        85 ~~~   87 (103)
T d2cpya1          85 TLE   87 (103)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            653

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=1.7e-18  Score=110.79  Aligned_cols=71  Identities=25%  Similarity=0.411  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeCC
Q 030010           26 LYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGTN  102 (184)
Q Consensus        26 l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~~  102 (184)
                      |||+|||+++++++|+++|++|| +..+.+.     +.++||||+|.+.++|++|++.||+..+.|++|+|++++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555543     45789999999999999999999999999999999999754

>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=99.76  E-value=4.2e-18  Score=112.11  Aligned_cols=80  Identities=18%  Similarity=0.181  Sum_probs=71.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCceEE
Q 030010           18 SAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY--NNVQLDGKPMK   95 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l--~g~~~~g~~i~   95 (184)
                      ....|+++|||+|||..+++++|+++|++||.|..+.+..+     ++||||+|.+.++|++|++.+  ++..+.|++|+
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            34668999999999999999999999999999999998754     469999999999999999865  56899999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |.+++.+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9998754

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.8e-18  Score=114.90  Aligned_cols=80  Identities=19%  Similarity=0.172  Sum_probs=70.1

Q ss_pred             CCCCEEEEcCCCCCC-CH----HHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           21 ETGTKLYISNLDYGV-SN----EDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        21 ~~~~~l~V~nLp~~~-te----~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      ..+++|||+||+..+ ++    ++|+++|++||.|..++++.     .++||||+|.+.++|.+||+.||+..|.|+.|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            457899999999876 33    56999999999999999874     366999999999999999999999999999999


Q ss_pred             EEEeeCCCCC
Q 030010           96 IEIVGTNIAT  105 (184)
Q Consensus        96 V~~~~~~~~~  105 (184)
                      |.++++....
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999865543

>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=99.72  E-value=1.8e-17  Score=111.49  Aligned_cols=80  Identities=24%  Similarity=0.302  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHH--HhCCCccCCceEE
Q 030010           19 AIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVK--RYNNVQLDGKPMK   95 (184)
Q Consensus        19 ~~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~--~l~g~~~~g~~i~   95 (184)
                      ...++++|||+|||.. +|+++|.++|++||.|..|.++.+     +++|||+|.+.++|.+||+  .+++..|.|+.|+
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            3456789999999985 899999999999999999999854     5699999999999999997  5778899999999


Q ss_pred             EEEeeCCC
Q 030010           96 IEIVGTNI  103 (184)
Q Consensus        96 V~~~~~~~  103 (184)
                      |.+++...
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997543

>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=99.71  E-value=2.7e-17  Score=108.51  Aligned_cols=80  Identities=21%  Similarity=0.257  Sum_probs=70.9

Q ss_pred             CCCCCCCEEEEcCCCCC-CCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCceE
Q 030010           18 SAIETGTKLYISNLDYG-VSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRY--NNVQLDGKPM   94 (184)
Q Consensus        18 ~~~~~~~~l~V~nLp~~-~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l--~g~~~~g~~i   94 (184)
                      ...+++.+|||+|||.. +|+++|.++|++||.|..|.+..+     +++|||+|.+.++|..|++.|  ++..+.|++|
T Consensus         3 ~~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           3 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            34677899999999986 789999999999999999999755     358999999999999999966  6788999999


Q ss_pred             EEEEeeCC
Q 030010           95 KIEIVGTN  102 (184)
Q Consensus        95 ~V~~~~~~  102 (184)
                      +|++++..
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99999754

>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=99.70  E-value=6.8e-17  Score=119.29  Aligned_cols=85  Identities=18%  Similarity=0.313  Sum_probs=78.0

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEE
Q 030010           17 ASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMK   95 (184)
Q Consensus        17 ~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~   95 (184)
                      .......++|||+|||+.+++++|+++|+.||.|..+.|+.+. ++++++||||+|.+.++|++||+ +++..|.|+.|+
T Consensus        91 ~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~  169 (183)
T d1u1qa_          91 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCE  169 (183)
T ss_dssp             TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEE
T ss_pred             cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEE
Confidence            3455667899999999999999999999999999999999988 78999999999999999999996 788999999999


Q ss_pred             EEEeeCC
Q 030010           96 IEIVGTN  102 (184)
Q Consensus        96 V~~~~~~  102 (184)
                      |.++.++
T Consensus       170 V~~A~~k  176 (183)
T d1u1qa_         170 VRKALSK  176 (183)
T ss_dssp             EEECCCH
T ss_pred             EEecCCc
Confidence            9998764

>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=99.67  E-value=5.4e-19  Score=116.92  Aligned_cols=74  Identities=18%  Similarity=0.417  Sum_probs=64.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEE-----eC-CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEE
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIH-----YD-RSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIE   97 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~-----~~-~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~   97 (184)
                      ++|||+|||+.++|++|+++|++||.|..+.+.     .+ .++++++||||+|.+.++|++|++ ||+..|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            689999999999999999999999987655442     22 256789999999999999999995 99999999999996


Q ss_pred             E
Q 030010           98 I   98 (184)
Q Consensus        98 ~   98 (184)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.4e-18  Score=115.05  Aligned_cols=76  Identities=20%  Similarity=0.281  Sum_probs=71.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEe
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIV   99 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~   99 (184)
                      +.++|.+++..++|++|+++|++||+|..|.|+.+.+++++|||||+|.+.++|.+|++.||+..|.|++|+|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4578888888899999999999999999999988889999999999999999999999999999999999999985

>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=99.60  E-value=2.1e-15  Score=103.54  Aligned_cols=76  Identities=21%  Similarity=0.310  Sum_probs=65.0

Q ss_pred             CCCCEE-EEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCH-HHHHHHHHHhCCCccCCceEEEEE
Q 030010           21 ETGTKL-YISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRR-ADAVAAVKRYNNVQLDGKPMKIEI   98 (184)
Q Consensus        21 ~~~~~l-~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~-e~a~~Ai~~l~g~~~~g~~i~V~~   98 (184)
                      ..++.| ||+|||..+|+++|+++|++||+|..|.|+.+     ++||||.|.+. ++|..|+..|++..+.++.+.|.+
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            344555 99999999999999999999999999999844     67999999985 789999999999888877777776


Q ss_pred             eeC
Q 030010           99 VGT  101 (184)
Q Consensus        99 ~~~  101 (184)
                      ...
T Consensus        83 ~~~   85 (113)
T d1owxa_          83 EVL   85 (113)
T ss_dssp             EEC
T ss_pred             eec
Confidence            654

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.7e-15  Score=101.93  Aligned_cols=67  Identities=16%  Similarity=0.188  Sum_probs=59.3

Q ss_pred             CCCCCCEEEEcC--CCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 030010           19 AIETGTKLYISN--LDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLD   90 (184)
Q Consensus        19 ~~~~~~~l~V~n--Lp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~   90 (184)
                      ...++.+|||.|  ||..+|+++|+++|++||.|..|.+..+     ++||||+|.+.++|++|++.||+..|.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            445678899955  9999999999999999999999988754     569999999999999999999998773

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.3e-14  Score=97.15  Aligned_cols=84  Identities=14%  Similarity=0.264  Sum_probs=71.2

Q ss_pred             CCCCCCCCEEEEcCC--CCCC---------CHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           17 ASAIETGTKLYISNL--DYGV---------SNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        17 ~~~~~~~~~l~V~nL--p~~~---------te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      |+....+++|+|.||  |.++         .+++|++.|++||.|..|.+..+   ..+|++||+|.+.++|.+|+..||
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhC
Confidence            556677899999999  5432         13678899999999999988754   457899999999999999999999


Q ss_pred             CCccCCceEEEEEeeCCC
Q 030010           86 NVQLDGKPMKIEIVGTNI  103 (184)
Q Consensus        86 g~~~~g~~i~V~~~~~~~  103 (184)
                      +..|.|++|+|++..++.
T Consensus        79 g~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          79 GRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CcEECCEEEEEEEeCCcC
Confidence            999999999999987644

>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=99.53  E-value=2.8e-14  Score=104.96  Aligned_cols=77  Identities=23%  Similarity=0.402  Sum_probs=69.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEeeC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVGT  101 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~~  101 (184)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+. ++.+++||||+|.+.++|++|+. +++..+..+.+.+.....
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            689999999999999999999999999999999988 88999999999999999999996 466777888777776544

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.7e-14  Score=95.75  Aligned_cols=81  Identities=15%  Similarity=0.142  Sum_probs=69.1

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHHhhCCCeEEEEEEeCCC---CCcceEEEEEecCHHHHHHHHHHhCCC
Q 030010           21 ETGTKLYISNL--DYGVS--------NEDIKELFSEVGDLKRYSIHYDRS---GRSKGTAEVVYSRRADAVAAVKRYNNV   87 (184)
Q Consensus        21 ~~~~~l~V~nL--p~~~t--------e~~L~~~f~~~G~i~~v~i~~~~~---~~~~g~afV~F~~~e~a~~Ai~~l~g~   87 (184)
                      .|++.|.|.||  |..+.        .++|++.|++||.|..|.|..+..   ....|++||+|.+.++|.+|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46889999999  55432        356899999999999999987662   345689999999999999999999999


Q ss_pred             ccCCceEEEEEeeC
Q 030010           88 QLDGKPMKIEIVGT  101 (184)
Q Consensus        88 ~~~g~~i~V~~~~~  101 (184)
                      .++|+.|.|.+...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=4.4e-14  Score=91.07  Aligned_cols=73  Identities=8%  Similarity=0.084  Sum_probs=61.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCce-EEEEEee
Q 030010           22 TGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKP-MKIEIVG  100 (184)
Q Consensus        22 ~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~-i~V~~~~  100 (184)
                      ..+.|+|.+||++++++.| ++|++||+|.++++..     .++|+||+|.+.++|++||+ +|+..|.|+. |.|....
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~-----~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC-----CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            3567999999999887666 5799999999998753     36799999999999999995 8999999984 5677665


Q ss_pred             C
Q 030010          101 T  101 (184)
Q Consensus       101 ~  101 (184)
                      +
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=98.08  E-value=1.9e-05  Score=50.62  Aligned_cols=68  Identities=13%  Similarity=0.214  Sum_probs=58.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCC-CC--CcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 030010           24 TKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDR-SG--RSKGTAEVVYSRRADAVAAVKRYNNVQLDG   91 (184)
Q Consensus        24 ~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~-~~--~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g   91 (184)
                      ++|.|+.||+++||+++.+.+...+.+........+ +-  ....-|||.|.+.+++....+.++++.|.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            679999999999999999999999998888777766 32  235689999999999999999999988865

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.94  E-value=2.5e-05  Score=47.12  Aligned_cols=61  Identities=18%  Similarity=0.266  Sum_probs=52.9

Q ss_pred             HHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           38 EDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        38 ~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      +.|...|.+++.|.++.|.....+..  .|-|...+.++|+.|+..|+...|..++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34667789999999999876665554  68999999999999999999999999999999975

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.79  E-value=1.9e-05  Score=50.06  Aligned_cols=54  Identities=13%  Similarity=0.288  Sum_probs=47.8

Q ss_pred             HHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCceEEEEEee
Q 030010           39 DIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYNNVQLDGKPMKIEIVG  100 (184)
Q Consensus        39 ~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~g~~~~g~~i~V~~~~  100 (184)
                      +|.+.|.+||+|.-|+++.+       ..+|+|.+-++|.+|++ +++.++.|+.|+|....
T Consensus        40 ~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          40 ELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            57788899999999999855       68999999999999995 79999999999998654

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.70  E-value=0.0062  Score=38.78  Aligned_cols=65  Identities=20%  Similarity=0.213  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHhhCCCeEEEEEEeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030010           14 AGRASAIETGTKLYISNLDYGVSNEDIKELFSEVGDLKRYSIHYDRSGRSKGTAEVVYSRRADAVAAVKRYN   85 (184)
Q Consensus        14 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~f~~~G~i~~v~i~~~~~~~~~g~afV~F~~~e~a~~Ai~~l~   85 (184)
                      .+.+.+...-.-||.-..|......+|.++|+.||.|. |.++.+.      .|||...+.++++.++..+.
T Consensus         6 ~~G~d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_           6 SGGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSCCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             cCCCCCCCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc------eEEEEecCHHHHHHHHHHhc
Confidence            34455555666777778999999999999999999875 5555443      79999999999999887544