Citrus Sinensis ID: 026724

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230----
Protein Sequence
MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEccHHHHHHHHHcccccccEEEEEEcccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEcccccccccEEEEEEcccHHHHHHHHcccEEccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEccHHHHHHHHHcccEEcccEEEccEccccHHcccccccccccccccccccccccHHHHHcccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEcccccccccEEEEEEccHHHHHHHHHccccEcccEEEEEEEcccHHcccccccccccccccccccccHHHHHHHccccccEEEEEccccccccccccccccc
Coil and Loop (DISEMBL)
mpkdqgskahrgigfitfasadsVENLMVDThelggstvvvdratpkeddfrpvgrmshggygaYNAYISAATRYAalgaptlydhpgsfygrgessqrigkkifvgrlpqeatAEDLRRYFSRFGrildvyvpkrtghrgfgfVTFAEEVVADrvsrrsheicgqqvaidsatplddagpsqnfMMNAAetfggyggpmrtygrmygsldfddwgygmgsgrpsrgdwryrpy
Flexible Loop (DISEMBL)
mpkdqgskahrgiGFITFASADSVENLMVDTHELGgstvvvdratpkeddfrpvgrmshGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIfvgrlpqeataeDLRRYFSRFGrildvyvpkrtghrgfgFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGmgsgrpsrgdwryrpy
Low Complexity Region (SEG)
MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY
Disordered region (IsUnstruct)
***********GIGFITFASADSVENLMVDTHELGGSTVVVDRA******FRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAID*************FMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGM***************
Disordered Region (DISOPRED)
*PK***SKAHRGIGFITFASADSVENLMVDTHELGGSTVV**************************************************************KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVA**************************************G**************************
Disordered Region (DISEMBL)
*********HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY
Disordered Region (DISPRO)
*********HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED************YGAYNAYISAATRYAALGAPTL***************RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDD************ETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY
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	234	2.2.26 [Sep-21-2011]
Q9VVE5	369	RNA-binding protein Musas	yes	no	0.675	0.428	0.299	3e-12
P48809	421	Heterogeneous nuclear rib	no	no	0.709	0.394	0.251	1e-11
Q8W034	411	Heterogeneous nuclear rib	no	no	0.594	0.338	0.298	1e-10
O94432	474	Uncharacterized RNA-bindi	yes	no	0.534	0.263	0.282	2e-10
Q920Q6	346	RNA-binding protein Musas	yes	no	0.559	0.378	0.294	2e-10
Q96DH6	328	RNA-binding protein Musas	yes	no	0.559	0.399	0.294	3e-10
O43347	362	RNA-binding protein Musas	no	no	0.581	0.375	0.281	5e-10
Q28F51	409	TAR DNA-binding protein 4	yes	no	0.307	0.176	0.405	5e-10
Q8K3P4	362	RNA-binding protein Musas	no	no	0.581	0.375	0.281	7e-10
Q61474	362	RNA-binding protein Musas	no	no	0.581	0.375	0.281	7e-10

>sp|Q9VVE5|MSIR6_DROME RNA-binding protein Musashi homolog Rbp6 OS=Drosophila melanogaster GN=Rbp6 PE=2 SV=3

 Score = 72.0 bits (175), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 92/224 (41%), Gaps = 66/224 (29%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           KD  ++  RG GF+TF+  +SV+ ++   THEL G  V    A P+              
Sbjct: 62  KDPTTRRSRGFGFVTFSDPNSVDKVLTQGTHELDGKKVDPKVAFPRR------------- 108

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+    TR                           KKIFVG L    T ED++ Y
Sbjct: 109 -----AHPKMVTR--------------------------TKKIFVGGLSAPTTLEDVKSY 137

Query: 122 FSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPLD 177
           F +FG I D  +   K+T  HRGFGFVTF  E V D+V     HEI  + V    A P +
Sbjct: 138 FEQFGPIEDAMLMFDKQTNRHRGFGFVTFQSEDVVDKVCEIHFHEINNKMVECKKAQPKE 197

Query: 178 DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGS 221
              P+     N A+T            R  G   +D+  +G+G+
Sbjct: 198 VMLPA-----NLAKT------------RAAGRSAYDNIMWGLGT 224

RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system.
Drosophila melanogaster (taxid: 7227)

>sp|P48809|RB27C_DROME Heterogeneous nuclear ribonucleoprotein 27C OS=Drosophila melanogaster GN=Hrb27C PE=1 SV=2

 Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 89/215 (41%), Gaps = 49/215 (22%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           K+  S   RG GF+TFA   +V +++ +  H L G T+      PK  + R + +   GG
Sbjct: 40  KNNESGRSRGFGFVTFADPTNVNHVLQNGPHTLDGRTI-----DPKPCNPRTLQKPKKGG 94

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                  G K+F+G LP   T  DLR +
Sbjct: 95  ---------------------------------------GYKVFLGGLPSNVTETDLRTF 115

Query: 122 FSRFGRILDV---YVPKRTGHRGFGFVTFAEEVVADRVSRRSH-EICGQQVAIDSATPLD 177
           F+R+G++ +V   Y  ++   RGFGF++F EE   + V+   +  + G+QV I  A P D
Sbjct: 116 FNRYGKVTEVVIMYDQEKKKSRGFGFLSFEEESSVEHVTNERYINLNGKQVEIKKAEPRD 175

Query: 178 DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDF 212
            +G   +        +G  G     +G  +  ++ 
Sbjct: 176 GSGGQNSNNSTVGGAYGKLGNECSHWGPHHAPINM 210

This protein is a component of ribonucleosomes. Could be needed to organize a concentration gradient of a dorsalizing morphogen (Dm) originating in the germinal vesicle.

Drosophila melanogaster (taxid: 7227)

>sp|Q8W034|RNP1_ARATH Heterogeneous nuclear ribonucleoprotein 1 OS=Arabidopsis thaliana GN=RNP1 PE=1 SV=1

 Score = 66.6 bits (161), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 75/171 (43%), Gaps = 32/171 (18%)

Query: 11  RGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYIS 70
           RG GF+ F+    ++ ++ + H +    V V RA  +E+      +   G  G  N   S
Sbjct: 47  RGFGFVIFSDPSVLDRVLQEKHSIDTREVDVKRAMSREE------QQVSGRTGNLNTSRS 100

Query: 71  AATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD 130
           +                G  Y +        KKIFVG LP   T E+ R+YF  +G + D
Sbjct: 101 SG---------------GDAYNKT-------KKIFVGGLPPTLTDEEFRQYFEVYGPVTD 138

Query: 131 V---YVPKRTGHRGFGFVTFAEEVVADRVSRRS-HEICGQQVAIDSATPLD 177
           V   Y       RGFGFV+F  E   D V  ++ H++ G+QV +  A P D
Sbjct: 139 VAIMYDQATNRPRGFGFVSFDSEDAVDSVLHKTFHDLSGKQVEVKRALPKD 189

Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection.

Arabidopsis thaliana (taxid: 3702)

>sp|O94432|YHKF_SCHPO Uncharacterized RNA-binding protein C660.15 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC660.15 PE=4 SV=1

 Score = 66.2 bits (160), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 73/177 (41%), Gaps = 52/177 (29%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGY 62
           +D  +   RG GF+TF +   V  +M   H L G  +   RA P+E+             
Sbjct: 196 RDSTTGRSRGFGFLTFKNPKCVNEVMSKEHHLDGKIIDPKRAIPREE------------- 242

Query: 63  GAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYF 122
                                              Q    K+FVG +P + T E+ R +F
Sbjct: 243 -----------------------------------QEKTAKMFVGGVPGDCTEEEFRNFF 267

Query: 123 SRFGRILD--VYVPKRTGH-RGFGFVTFAEE-VVADRVSRRSHEICGQQVAIDSATP 175
           ++FGR+LD  + + K TG  RGFGFVT+  E  V   +S+    I G+ V +  ATP
Sbjct: 268 NQFGRVLDATLMMDKDTGRPRGFGFVTYENESAVEATMSQPYITIHGKPVEVKRATP 324

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q920Q6|MSI2H_MOUSE RNA-binding protein Musashi homolog 2 OS=Mus musculus GN=Msi2 PE=1 SV=1

 Score = 65.9 bits (159), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 73/180 (40%), Gaps = 49/180 (27%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDTH-ELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+TFA   SV+ ++   H EL   T+    A P+    + V R     
Sbjct: 54  RDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRT---- 109

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG L      ED+++Y
Sbjct: 110 ----------------------------------------KKIFVGGLSANTVVEDVKQY 129

Query: 122 FSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPLD 177
           F +FG++ D  +   K T  HRGFGFVTF  E V ++V     HEI  + V    A P +
Sbjct: 130 FEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKKAQPKE 189

RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Mus musculus (taxid: 10090)

>sp|Q96DH6|MSI2H_HUMAN RNA-binding protein Musashi homolog 2 OS=Homo sapiens GN=MSI2 PE=1 SV=1

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 73/180 (40%), Gaps = 49/180 (27%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDTH-ELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+TFA   SV+ ++   H EL   T+    A P+    + V R     
Sbjct: 54  RDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRT---- 109

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG L      ED+++Y
Sbjct: 110 ----------------------------------------KKIFVGGLSANTVVEDVKQY 129

Query: 122 FSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPLD 177
           F +FG++ D  +   K T  HRGFGFVTF  E V ++V     HEI  + V    A P +
Sbjct: 130 FEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKKAQPKE 189

RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Homo sapiens (taxid: 9606)

>sp|O43347|MSI1H_HUMAN RNA-binding protein Musashi homolog 1 OS=Homo sapiens GN=MSI1 PE=1 SV=1

 Score = 64.7 bits (156), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 75/185 (40%), Gaps = 49/185 (26%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+TF     V+ ++  + HEL   T+    A P+    + V R     
Sbjct: 53  RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRT---- 108

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG L    T ED+++Y
Sbjct: 109 ----------------------------------------KKIFVGGLSVNTTVEDVKQY 128

Query: 122 FSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPLD 177
           F +FG++ D  +   K T  HRGFGFVTF  E + ++V     HEI  + V    A P +
Sbjct: 129 FEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKE 188

Query: 178 DAGPS 182
              P+
Sbjct: 189 VMSPT 193

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Homo sapiens (taxid: 9606)

>sp|Q28F51|TADBP_XENTR TAR DNA-binding protein 43 OS=Xenopus tropicalis GN=tardbp PE=2 SV=1

 Score = 64.7 bits (156), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 49/74 (66%), Gaps = 2/74 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           +K+FVGR  ++ +AE+LR++FS++G ++DV++PK    R F FVTFA++ VA  +     
Sbjct: 191 RKVFVGRCTEDMSAEELRQFFSQYGEVVDVFIPK--PFRAFAFVTFADDQVAQSLCGEDL 248

Query: 162 EICGQQVAIDSATP 175
            I G  V + +A P
Sbjct: 249 IIKGVSVHVSTAEP 262

Probably involved in transcriptional repression.

Xenopus tropicalis (taxid: 8364)

>sp|Q8K3P4|MSI1H_RAT RNA-binding protein Musashi homolog 1 OS=Rattus norvegicus GN=Msi1 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 74/185 (40%), Gaps = 49/185 (26%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+TF     V+ ++  + HEL   T+    A P+    + V R     
Sbjct: 53  RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRT---- 108

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG L    T ED++ Y
Sbjct: 109 ----------------------------------------KKIFVGGLSVNTTVEDVKHY 128

Query: 122 FSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPLD 177
           F +FG++ D  +   K T  HRGFGFVTF  E + ++V     HEI  + V    A P +
Sbjct: 129 FEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKE 188

Query: 178 DAGPS 182
              P+
Sbjct: 189 VMSPT 193

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Rattus norvegicus (taxid: 10116)

>sp|Q61474|MSI1H_MOUSE RNA-binding protein Musashi homolog 1 OS=Mus musculus GN=Msi1 PE=1 SV=1

 Score = 64.3 bits (155), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 74/185 (40%), Gaps = 49/185 (26%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+TF     V+ ++  + HEL   T+    A P+    + V R     
Sbjct: 53  RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRT---- 108

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG L    T ED++ Y
Sbjct: 109 ----------------------------------------KKIFVGGLSVNTTVEDVKHY 128

Query: 122 FSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPLD 177
           F +FG++ D  +   K T  HRGFGFVTF  E + ++V     HEI  + V    A P +
Sbjct: 129 FEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKE 188

Query: 178 DAGPS 182
              P+
Sbjct: 189 VMSPT 193

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

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	234
255565200	359	RNA-binding protein, putative [Ricinus c	1.0	0.651	0.860	1e-115
359480888	359	PREDICTED: uncharacterized RNA-binding p	1.0	0.651	0.848	1e-113
224094314	367	predicted protein [Populus trichocarpa]	1.0	0.637	0.813	1e-110
224084344	367	predicted protein [Populus trichocarpa]	1.0	0.637	0.804	1e-110
356496896	362	PREDICTED: DAZ-associated protein 1-like	0.991	0.640	0.818	1e-109
356541820	365	PREDICTED: DAZ-associated protein 1-like	0.987	0.632	0.792	1e-104
449460598	377	PREDICTED: RNA-binding protein Musashi h	1.0	0.620	0.777	1e-101
217074298	397	unknown [Medicago truncatula] gi|3885030	0.982	0.579	0.770	9e-98
357482897	403	RNA-binding protein [Medicago truncatula	1.0	0.580	0.676	9e-96
358349448	371	RNA-binding protein [Medicago truncatula	1.0	0.630	0.714	7e-94

>gi|255565200|ref|XP_002523592.1| RNA-binding protein, putative [Ricinus communis] gi|223537154|gb|EEF38787.1| RNA-binding protein, putative [Ricinus communis]

 Score =  419 bits (1078), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 204/237 (86%), Positives = 216/237 (91%), Gaps = 3/237 (1%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           MPKD  SKAHRGIGFITFASADSV++LM DTHELGGSTVVVDRATPKEDDFRPVGRM+HG
Sbjct: 123 MPKDHSSKAHRGIGFITFASADSVDSLMADTHELGGSTVVVDRATPKEDDFRPVGRMAHG 182

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
           GYGAYNAYISAATRYAALGAPTLYDHPG  YG GE ++ +GKKIFVGRLPQEAT EDLR+
Sbjct: 183 GYGAYNAYISAATRYAALGAPTLYDHPGPMYGTGEPARGVGKKIFVGRLPQEATPEDLRQ 242

Query: 121 YFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLD 177
           YF RFG ILDVYV   PKRTGHRGFGFVTFAEE VADRVSRRSHEICG QVAIDSATP+D
Sbjct: 243 YFGRFGHILDVYVPKDPKRTGHRGFGFVTFAEEGVADRVSRRSHEICGHQVAIDSATPID 302

Query: 178 DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY 234
           DAGPS NFMMNAA +FGGYGGP+R +GRMYGSLD+DDWGYGMGS RPSR DWRYRPY
Sbjct: 303 DAGPSGNFMMNAAPSFGGYGGPLRNFGRMYGSLDYDDWGYGMGSARPSRADWRYRPY 359

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480888|ref|XP_002282572.2| PREDICTED: uncharacterized RNA-binding protein C660.15-like isoform 1 [Vitis vinifera] gi|359480890|ref|XP_003632540.1| PREDICTED: uncharacterized RNA-binding protein C660.15-like isoform 2 [Vitis vinifera] gi|296082418|emb|CBI21423.3| unnamed protein product [Vitis vinifera]

 Score =  414 bits (1065), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 201/237 (84%), Positives = 219/237 (92%), Gaps = 3/237 (1%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           MPKD GSK HRGIGFITFASA+SV+NLMV+THELGGS VVVDRATPKE++FRPV R+  G
Sbjct: 123 MPKDHGSKGHRGIGFITFASAESVDNLMVETHELGGSAVVVDRATPKEEEFRPVSRVPQG 182

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
           GYGAYNAYI+AATRYAALGAPTLYDHPGS YGRGES++ +GKKIFVGRLPQEA+AEDLR+
Sbjct: 183 GYGAYNAYITAATRYAALGAPTLYDHPGSVYGRGESTRAMGKKIFVGRLPQEASAEDLRQ 242

Query: 121 YFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLD 177
           YF RFGRILDVYV   PKR+GHRGFGFVTFAE+ VADRVSRRSHEICGQQVAIDSATPLD
Sbjct: 243 YFGRFGRILDVYVPKDPKRSGHRGFGFVTFAEDGVADRVSRRSHEICGQQVAIDSATPLD 302

Query: 178 DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYRPY 234
           DAG S NFMM++AE FGG+GGPMRTYGRMYGSLDFDDWGYG+G GRPSR DWRYRPY
Sbjct: 303 DAGSSGNFMMDSAEPFGGFGGPMRTYGRMYGSLDFDDWGYGIGGGRPSRADWRYRPY 359

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224094314|ref|XP_002310138.1| predicted protein [Populus trichocarpa] gi|222853041|gb|EEE90588.1| predicted protein [Populus trichocarpa]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 200/246 (81%), Positives = 214/246 (86%), Gaps = 12/246 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           MPKD  SKAHRGIGFIT+ASADSV+NLM +THELGGSTVVVDRATPKEDDFRP GRM+ G
Sbjct: 122 MPKDHSSKAHRGIGFITYASADSVDNLMAETHELGGSTVVVDRATPKEDDFRPNGRMAPG 181

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
           GYGAYNAYISAATRYAALGAPTLYDHPG FYGRGESS+ +GKKIFVGRLPQEA+AEDLR+
Sbjct: 182 GYGAYNAYISAATRYAALGAPTLYDHPGPFYGRGESSRGMGKKIFVGRLPQEASAEDLRQ 241

Query: 121 YFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLD 177
           YF RFG ILDVYV   PKRTGHRGFGFVTFAE+ VADRVSRRSHEICG QVAIDSATP+D
Sbjct: 242 YFGRFGHILDVYVPKDPKRTGHRGFGFVTFAEDGVADRVSRRSHEICGHQVAIDSATPID 301

Query: 178 DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDD---------WGYGMGSGRPSRGD 228
           DAGPS NFMM+  E FG Y GPMR +GRMYG+LD+DD         WGYGMGS RPSR D
Sbjct: 302 DAGPSGNFMMSGPEPFGSYAGPMRNFGRMYGTLDYDDASAYMVPSKWGYGMGSARPSRAD 361

Query: 229 WRYRPY 234
           WRYRPY
Sbjct: 362 WRYRPY 367

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224084344|ref|XP_002307266.1| predicted protein [Populus trichocarpa] gi|222856715|gb|EEE94262.1| predicted protein [Populus trichocarpa]

 Score =  402 bits (1033), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 198/246 (80%), Positives = 215/246 (87%), Gaps = 12/246 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           MPKD  SKAHRGIGFIT+ASADSV++LM +THELGGSTVVVDRATPKEDDFRP+ R + G
Sbjct: 122 MPKDHSSKAHRGIGFITYASADSVDSLMAETHELGGSTVVVDRATPKEDDFRPIARTAPG 181

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
           GYGAYNAYISAATRYAALGAPTLYDHPG FYGRGESS+ +GKKIFVGRLPQEA+ EDLR+
Sbjct: 182 GYGAYNAYISAATRYAALGAPTLYDHPGPFYGRGESSRGMGKKIFVGRLPQEASTEDLRQ 241

Query: 121 YFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLD 177
           YF RFG I+DVYV   PKRTGHRGFGFVTFAE+ VADRVSRRSHEICG QVAIDSATP+D
Sbjct: 242 YFGRFGHIIDVYVPKDPKRTGHRGFGFVTFAEDGVADRVSRRSHEICGHQVAIDSATPID 301

Query: 178 DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDD---------WGYGMGSGRPSRGD 228
           DAGPS NFMM+A E FGGYGGPMR +GRMYG+LD+DD         WGYGMGS RPSR D
Sbjct: 302 DAGPSGNFMMSAPEPFGGYGGPMRNFGRMYGTLDYDDAGAYMVPSKWGYGMGSARPSRAD 361

Query: 229 WRYRPY 234
           WRYRPY
Sbjct: 362 WRYRPY 367

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496896|ref|XP_003517301.1| PREDICTED: DAZ-associated protein 1-like [Glycine max]

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 198/242 (81%), Positives = 215/242 (88%), Gaps = 10/242 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRM--- 57
           MPKDQGSK HRGIGFITFASADSVENLM +THELGGS VVVDRATPK+DDF+P+GRM   
Sbjct: 123 MPKDQGSKMHRGIGFITFASADSVENLMSETHELGGSAVVVDRATPKDDDFKPIGRMPLP 182

Query: 58  --SHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATA 115
             + GGYGAYNAYISAATRYAALGAPTLYD PG  YGRG+ S+R  KKIFVGRLP EAT+
Sbjct: 183 PPTQGGYGAYNAYISAATRYAALGAPTLYDQPGPIYGRGDPSRRTSKKIFVGRLPPEATS 242

Query: 116 EDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDS 172
           +DLR+YF RFGRILDVYVP   KRTGHRGFGFVTFAE+ VADRVSRRSHEICG QVAIDS
Sbjct: 243 DDLRQYFGRFGRILDVYVPRDPKRTGHRGFGFVTFAEDGVADRVSRRSHEICGHQVAIDS 302

Query: 173 ATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRYR 232
           ATP+DDAGPS NFMMN+ E+FGGYGGP+R+YGRMYGSLDFDDWGYG+  GRPSR DWRYR
Sbjct: 303 ATPVDDAGPSGNFMMNSMESFGGYGGPVRSYGRMYGSLDFDDWGYGI--GRPSRADWRYR 360

Query: 233 PY 234
           PY
Sbjct: 361 PY 362

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541820|ref|XP_003539370.1| PREDICTED: DAZ-associated protein 1-like [Glycine max]

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 195/246 (79%), Positives = 212/246 (86%), Gaps = 15/246 (6%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSH- 59
           MPKDQGSK HRGIGFITFASADSVENLM +THELGGS VVVDRATPK+DDF+P+GRM   
Sbjct: 123 MPKDQGSKMHRGIGFITFASADSVENLMSETHELGGSAVVVDRATPKDDDFKPMGRMPPP 182

Query: 60  -------GGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQE 112
                  GGYGAYNAYISAATRYAALGAPTLYDHPG  YGRG++ +R  KKIFVGRLP E
Sbjct: 183 PPPPPQGGGYGAYNAYISAATRYAALGAPTLYDHPGPIYGRGDA-RRTSKKIFVGRLPPE 241

Query: 113 ATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVA 169
           AT++DLR+YF RFGRILDVYVP   KR GHRGFGFVTFAE+  ADRVSRRSHEICG  VA
Sbjct: 242 ATSDDLRQYFGRFGRILDVYVPRDPKRAGHRGFGFVTFAEDGAADRVSRRSHEICGHPVA 301

Query: 170 IDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSR-GD 228
           IDSATP+DDAGPS NFMMN+ E+FGGYGGP+R+YGRMYGSLDFDDWGYG+  GRPSR  D
Sbjct: 302 IDSATPVDDAGPSGNFMMNSMESFGGYGGPVRSYGRMYGSLDFDDWGYGI--GRPSRAAD 359

Query: 229 WRYRPY 234
           WRYRPY
Sbjct: 360 WRYRPY 365

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460598|ref|XP_004148032.1| PREDICTED: RNA-binding protein Musashi homolog 1-like [Cucumis sativus] gi|449502733|ref|XP_004161727.1| PREDICTED: RNA-binding protein Musashi homolog 1-like [Cucumis sativus]

 Score =  372 bits (954), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 199/256 (77%), Positives = 215/256 (83%), Gaps = 22/256 (8%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSH- 59
           MPKDQGSK HRGIGFITFAS+DSVENLM DTHELGGS VVVDRATPK+DDFRP+G+M   
Sbjct: 122 MPKDQGSKTHRGIGFITFASSDSVENLMADTHELGGSNVVVDRATPKDDDFRPIGKMPQG 181

Query: 60  -----GGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESS-----QRIGKKIFVGRL 109
                GGYGAYNAYISAATRYAALGAPTLYDHPGS YG    +     + +GKKIFVGRL
Sbjct: 182 GGGGGGGYGAYNAYISAATRYAALGAPTLYDHPGSVYGSMSPTVPLEFRGMGKKIFVGRL 241

Query: 110 PQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQ 166
           PQEA+A+DLR+YF RFGRILDVYV   PKR+GHRGFGFVTFAE+ VADRVSRRSHEICGQ
Sbjct: 242 PQEASADDLRQYFGRFGRILDVYVPKDPKRSGHRGFGFVTFAEDGVADRVSRRSHEICGQ 301

Query: 167 QVAIDSATPLDD-------AGPSQNFMMN-AAETFGGYGGPMRTYGRMYGSLDFDDWGYG 218
           QVAIDSATPLDD       +G S  FMMN AA++FGGY GPMRTYGRMYGSLDFDDWGYG
Sbjct: 302 QVAIDSATPLDDAGAGAGASGASGTFMMNSAADSFGGYVGPMRTYGRMYGSLDFDDWGYG 361

Query: 219 MGSGRPSRGDWRYRPY 234
           +G GRPSR DWRYRPY
Sbjct: 362 IGGGRPSRADWRYRPY 377

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074298|gb|ACJ85509.1| unknown [Medicago truncatula] gi|388503058|gb|AFK39595.1| unknown [Medicago truncatula]

 Score =  362 bits (928), Expect = 9e-98,   Method: Compositional matrix adjust.
 Identities = 181/235 (77%), Positives = 201/235 (85%), Gaps = 5/235 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           MPKDQGSK HRGIGFITF +A+SVENLM +THELGGS VVVDRATPKEDD +P GRMS G
Sbjct: 123 MPKDQGSKMHRGIGFITFGNAESVENLMSETHELGGSAVVVDRATPKEDDVKPTGRMSQG 182

Query: 61  G-YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLR 119
           G YGAYNAYIS ATRYAALGAPTLYDHPG  YGRGE  +RI KKIFVGRLP EA +EDLR
Sbjct: 183 GGYGAYNAYISTATRYAALGAPTLYDHPGPIYGRGEPRRRISKKIFVGRLPPEANSEDLR 242

Query: 120 RYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPL 176
           +YF RFGRI DV +   PKRTGHRGFGFVTFA+E VADRVS R HEICG +VAIDSATP+
Sbjct: 243 QYFGRFGRIEDVCIPRDPKRTGHRGFGFVTFADEGVADRVSLRPHEICGHEVAIDSATPV 302

Query: 177 DDAGPSQNFMM-NAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWR 230
           DDA PS NFMM N+ E+FGGYGGP+R+YGRMYG LD+DDWGYG+ S RPSR +++
Sbjct: 303 DDARPSGNFMMNNSMESFGGYGGPVRSYGRMYGGLDYDDWGYGVPSVRPSRAEYQ 357

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357482897|ref|XP_003611735.1| RNA-binding protein [Medicago truncatula] gi|355513070|gb|AES94693.1| RNA-binding protein [Medicago truncatula]

 Score =  355 bits (911), Expect = 9e-96,   Method: Compositional matrix adjust.
 Identities = 190/281 (67%), Positives = 207/281 (73%), Gaps = 47/281 (16%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPK--EDDFRPVGRMS 58
           MPKDQGSK HRGIGFITF +A+SVENLM +THELGGS VVVDRATPK  EDD +P GRMS
Sbjct: 123 MPKDQGSKMHRGIGFITFGNAESVENLMSETHELGGSAVVVDRATPKAREDDVKPTGRMS 182

Query: 59  HGG-YGAYNAYISAATRYAALGAPTLYDHPGSFYG----RGESSQRIGKKIFVGRLPQEA 113
            GG YGAYNAYIS ATRYAALGAPTLYDHPG  YG    RGE  +RI KKIFVGRLP EA
Sbjct: 183 QGGGYGAYNAYISTATRYAALGAPTLYDHPGPIYGSKHGRGEPRRRISKKIFVGRLPPEA 242

Query: 114 TAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAI 170
            +EDLR+YF RFGRI DVY+P   KRTGHRGFGFVTFA+E VADRVS R HEICG +VAI
Sbjct: 243 NSEDLRQYFGRFGRIEDVYIPRDPKRTGHRGFGFVTFADEGVADRVSLRPHEICGHEVAI 302

Query: 171 DSATPLDDAGPSQNFMM-NAAETFGGYGGPMRTYGRMYGSLDFDDWGYGMGS-------- 221
           DSATP+DDA PS NFMM N+ E+FGGYGGP+R+YGRMYG LD+DDWGYG+ S        
Sbjct: 303 DSATPVDDARPSGNFMMNNSMESFGGYGGPVRSYGRMYGGLDYDDWGYGVPSVRPSRAEY 362

Query: 222 ----------------------------GRPSRGDWRYRPY 234
                                       GRPSR DWRYRPY
Sbjct: 363 QEQLGRPSRADYQEQIGRPSRADYQEHIGRPSRADWRYRPY 403

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358349448|ref|XP_003638749.1| RNA-binding protein [Medicago truncatula] gi|355504684|gb|AES85887.1| RNA-binding protein [Medicago truncatula]

 Score =  348 bits (894), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 178/249 (71%), Positives = 199/249 (79%), Gaps = 15/249 (6%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRM--S 58
           MPKD+GSK HRGIGFITFA+ADSVENLM +THELGGS VVVDRATPKEDDF+P+GR    
Sbjct: 123 MPKDRGSKTHRGIGFITFATADSVENLMKETHELGGSDVVVDRATPKEDDFKPIGRTRTP 182

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
             GY AY+ YI A+TRYAALGAPT+YD P S YGRGE ++ I KKIFVGRLP EAT EDL
Sbjct: 183 QLGYSAYSTYIPASTRYAALGAPTMYDRPSSIYGRGEPARGISKKIFVGRLPPEATTEDL 242

Query: 119 RRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATP 175
           R YF RFG ILDVY+P   KR GHRGFGFVTFA+  VADRVSRR HEICGQ+VAIDSA P
Sbjct: 243 RLYFGRFGHILDVYIPRDVKRPGHRGFGFVTFADSGVADRVSRRPHEICGQEVAIDSAAP 302

Query: 176 LDDAGPSQNFMMNAAETFGGYGG---------PMRTYGRMYGSLDFDDWGYGMGSGRPSR 226
           LD+AGPS N M+N+ ++F GYGG         P+R+YGRMY SLDFDD GYG+ S RPSR
Sbjct: 303 LDEAGPSGNTMLNSMDSFRGYGGPVRPYFDESPVRSYGRMYNSLDFDDLGYGVASRRPSR 362

Query: 227 -GDWRYRPY 234
             DWRYRPY
Sbjct: 363 TTDWRYRPY 371

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	234
TAIR|locus:2115169	379	AT4G36960 [Arabidopsis thalian	0.747	0.461	0.726	2e-77
UNIPROTKB|D6RBZ0	327	HNRNPAB "Heterogeneous nuclear	0.559	0.400	0.345	4.7e-18
UNIPROTKB|E9PTS0	331	Hnrnpab "Protein Hnrnpab" [Rat	0.559	0.395	0.345	5e-18
UNIPROTKB|Q9QX81	332	Hnrnpab "RCG34663, isoform CRA	0.559	0.394	0.345	5.1e-18
TAIR|locus:2129590	411	AT4G14300 [Arabidopsis thalian	0.547	0.311	0.357	2.5e-17
ZFIN|ZDB-GENE-040426-2516	309	zgc:77052 "zgc:77052" [Danio r	0.551	0.417	0.342	6e-17
WB|WBGene00003423	320	msi-1 [Caenorhabditis elegans	0.431	0.315	0.4	8.4e-17
UNIPROTKB|F1NIB4	212	HNRNPAB "Uncharacterized prote	0.525	0.580	0.366	9.8e-17
TAIR|locus:2173967	460	AT5G55550 [Arabidopsis thalian	0.487	0.247	0.373	1.6e-16
ASPGD|ASPL0000063757	559	AN10941 [Emericella nidulans (	0.311	0.130	0.434	1e-15

TAIR|locus:2115169 AT4G36960 [Arabidopsis thaliana (taxid:3702)]

 Score = 693 (249.0 bits), Expect = 2.0e-77, Sum P(2) = 2.0e-77
 Identities = 133/183 (72%), Positives = 152/183 (83%)

Query:    60 GGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQR-IGKKIFVGRLPQEATAEDL 118
             GGYGAY+AYISAATRYAALGAPTLYD+P +FYGRGE + R IG KIFVGRLPQEA+ +DL
Sbjct:   197 GGYGAYDAYISAATRYAALGAPTLYDNPATFYGRGEPTTRGIGNKIFVGRLPQEASVDDL 256

Query:   119 RRYFSRFGRILDVYVPK---RTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATP 175
             R YF RFG I D Y+PK   R+GHRGFGFVTFAE  VADRV+RRSHEICGQ+VAIDSATP
Sbjct:   257 RDYFGRFGHIQDAYIPKDPKRSGHRGFGFVTFAENGVADRVARRSHEICGQEVAIDSATP 316

Query:   176 LDDAGPSQ--NFMMNAA--ETFGGYGGPMRTYGRMYGSLDFDDWGYGMGSGRPSRGDWRY 231
             LD+AGPS   + M++++  E FGGYGGPMR +GRMYG +  DDWGYGM + RPSR D RY
Sbjct:   317 LDEAGPSAGASSMLSSSRPEYFGGYGGPMRAFGRMYGGMSLDDWGYGMPNARPSRPDRRY 376

Query:   232 RPY 234
             RPY
Sbjct:   377 RPY 379

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|D6RBZ0 HNRNPAB "Heterogeneous nuclear ribonucleoprotein A/B" [Homo sapiens (taxid:9606)]

 Score = 173 (66.0 bits), Expect = 4.7e-18, Sum P(2) = 4.7e-18
 Identities = 49/142 (34%), Positives = 66/142 (46%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRV-S 157
             KKIFVG L  EAT E +R YF  FG I  + +P   K    RGF F+TF EE    +V  
Sbjct:   154 KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKLNKRRGFVFITFKEEEPVKKVLE 213

Query:   158 RRSHEICGQQVAIDSATPLD-----DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDF 212
             ++ H + G +  I  A P +       G       N      G GG  +++ + YG+   
Sbjct:   214 KKFHTVSGSKCEIKVAQPKEVYQQQQYGSGGRGNRNRGNRGSG-GGQSQSWNQGYGNYWN 272

Query:   213 DDWGYGMGSGRPSRGDWRYRPY 234
               +GY  G G P  G + Y PY
Sbjct:   273 QGYGYQQGYG-PGYGGYDYSPY 293

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|E9PTS0 Hnrnpab "Protein Hnrnpab" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 5.0e-18, Sum P(2) = 5.0e-18
 Identities = 49/142 (34%), Positives = 69/142 (48%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYV-PKRTGHRGFGFVTFAEEVVADRV-S 157
             KKIFVG L  EAT E +R YF +FG I  +++ + PK    RGF F+TF EE    +V  
Sbjct:   158 KKIFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITFKEEDPVKKVLE 217

Query:   158 RRSHEICGQQVAIDSATPLD-----DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDF 212
             ++ H + G +  I  A P +       G       N      G GG  +++ + YG+   
Sbjct:   218 KKFHTVSGSKCEIKVAQPKEVYQQQQYGSGGRGNRNRGNRGSG-GGQSQSWNQGYGNYWN 276

Query:   213 DDWGYGMGSGRPSRGDWRYRPY 234
               +GY  G G P  G + Y PY
Sbjct:   277 QGYGYQQGYG-PGYGGYDYSPY 297

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9QX81 Hnrnpab "RCG34663, isoform CRA_a" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 5.1e-18, Sum P(2) = 5.1e-18
 Identities = 49/142 (34%), Positives = 69/142 (48%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYV-PKRTGHRGFGFVTFAEEVVADRV-S 157
             KKIFVG L  EAT E +R YF +FG I  +++ + PK    RGF F+TF EE    +V  
Sbjct:   159 KKIFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITFKEEDPVKKVLE 218

Query:   158 RRSHEICGQQVAIDSATPLD-----DAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDF 212
             ++ H + G +  I  A P +       G       N      G GG  +++ + YG+   
Sbjct:   219 KKFHTVSGSKCEIKVAQPKEVYQQQQYGSGGRGNRNRGNRGSG-GGQSQSWNQGYGNYWN 277

Query:   213 DDWGYGMGSGRPSRGDWRYRPY 234
               +GY  G G P  G + Y PY
Sbjct:   278 QGYGYQQGYG-PGYGGYDYSPY 298

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001837 "epithelial to mesenchymal transition" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0043565 "sequence-specific DNA binding" evidence=ISS

TAIR|locus:2129590 AT4G14300 [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 2.5e-17, Sum P(2) = 2.5e-17
 Identities = 49/137 (35%), Positives = 70/137 (51%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADRVSR 158
             KKIFVG LP   T E+ R+YF  +G + DV +   + T   RGFGFV+F  E   D V  
Sbjct:   110 KKIFVGGLPPTLTDEEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVSFDSEDAVDSVLH 169

Query:   159 RS-HEICGQQVAIDSATPLD--DAGPSQNFMMNAAETFGGYGGPMRTY-GRMYGSLDFDD 214
             ++ H++ G+QV +  A P D    G  ++     +  + GYGG   +Y GRM  +     
Sbjct:   170 KTFHDLSGKQVEVKRALPKDANPGGGGRSMGGGGSGGYQGYGGNESSYDGRMDSNRFLQH 229

Query:   215 WGYGMGSGRPSRGDWRY 231
                 +G+G PS G   Y
Sbjct:   230 --QSVGNGLPSYGSSGY 244

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=RCA

ZFIN|ZDB-GENE-040426-2516 zgc:77052 "zgc:77052" [Danio rerio (taxid:7955)]

 Score = 170 (64.9 bits), Expect = 6.0e-17, Sum P(2) = 6.0e-17
 Identities = 48/140 (34%), Positives = 67/140 (47%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRV-S 157
             KKIFVG L  E T E +R YF  FG I  + +P   K +  RGF F+TF EE    ++  
Sbjct:   129 KKIFVGGLNPETTEEKIREYFGSFGEIETIELPTDPKTSKRRGFVFITFKEEFAVKKILE 188

Query:   158 RRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFG---GYGGPMRTYGRMYGSLDFDD 214
             ++ H +CG +  I  A P  +    Q F        G   G GGP +++ + Y +  + +
Sbjct:   189 KKYHNVCGSKCEIKIAQP-KEIYQQQQFGARGGGFGGRGRGRGGPGQSWNQGYNN--YWN 245

Query:   215 WGYGMGSGRPSRGDWRYRPY 234
              GYG G G    G   Y  Y
Sbjct:   246 QGYG-GQGYGYGGQQGYGGY 264

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

WB|WBGene00003423 msi-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 167 (63.8 bits), Expect = 8.4e-17, Sum P(2) = 8.4e-17
 Identities = 42/105 (40%), Positives = 56/105 (53%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR 158
             KK+F+G L   +T ED+++YF  +G++ D  +   K T  HRGFGFVTF  + VAD+V  
Sbjct:   134 KKVFIGGLSATSTLEDMKQYFETYGKVEDAMLMFDKATQRHRGFGFVTFDSDEVADKVCE 193

Query:   159 -RSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRT 202
                HEI G+ V    A P +   P Q     AA     YG P  T
Sbjct:   194 IHFHEINGKMVECKKAQPKEVMLPVQLNKSRAAAARNLYGMPPET 238

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1NIB4 HNRNPAB "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 156 (60.0 bits), Expect = 9.8e-17, Sum P(2) = 9.8e-17
 Identities = 51/139 (36%), Positives = 63/139 (45%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRV-S 157
             KKIFVG L  EAT E +R YF  FG I  + +P   K    RGF F+TF EE    +V  
Sbjct:    84 KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 143

Query:   158 RRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGY 217
             ++ H + G +  I  A P  +    Q F        G YGG  R  GR  G        Y
Sbjct:   144 KKFHNVSGSKCEIKVAQP-KEVYQQQQFSSGGGR--GSYGGRGRG-GRGGGQ---GSANY 196

Query:   218 GMGSGRPSRGDWR--YRPY 234
             G     P RG  +  Y+PY
Sbjct:   197 GK---TPRRGGHQNNYKPY 212

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

TAIR|locus:2173967 AT5G55550 [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 1.6e-16, Sum P(2) = 1.6e-16
 Identities = 46/123 (37%), Positives = 61/123 (49%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADRVSR 158
             KKIFVG LP   T E+ + YF +FG I DV V     T   RGFGF+TF  +   DRV  
Sbjct:   110 KKIFVGGLPSSITEEEFKNYFDQFGTIADVVVMYDHNTQRPRGFGFITFDSDDAVDRVLH 169

Query:   159 RS-HEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGY 217
             ++ HE+ G+ V +  A P  +  P  N     A     YGG      RM  +  F+++  
Sbjct:   170 KTFHELNGKLVEVKRAVP-KEISPVSNIRSPLASGVN-YGGGSN---RMPANSYFNNFAP 224

Query:   218 GMG 220
             G G
Sbjct:   225 GPG 227

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

ASPGD|ASPL0000063757 AN10941 [Emericella nidulans (taxid:162425)]

 Score = 159 (61.0 bits), Expect = 1.0e-15, Sum P(3) = 1.0e-15
 Identities = 33/76 (43%), Positives = 47/76 (61%)

Query:   103 KIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFAEEVVADRVSRR 159
             KIFVG + QEAT +D +++F +FGR++D  + + K TG  RGFGFVTF  E   +    R
Sbjct:   195 KIFVGGVSQEATEQDFKQFFMQFGRVIDATLMIDKDTGRPRGFGFVTFDSEAAVEAALSR 254

Query:   160 SHEICGQQVAIDSATP 175
               EI G+ + +  A P
Sbjct:   255 PLEILGKTIEVKKAQP 270

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

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: estExt_fgenesh4_pm.C_LG_VII0327 hypothetical protein (368 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	234
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	8e-28
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-17
smart00360	73	smart00360, RRM, RNA recognition motif	1e-15
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-15
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-15
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-14
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-13
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-12
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-11
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-11
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-11
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-11
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	7e-11
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	7e-11
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	8e-11
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-10
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	4e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-10
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-10
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-09
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-09
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	4e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	6e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-09
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	8e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-08
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-08
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-08
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-08
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-08
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-08
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	3e-08
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-08
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	5e-08
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	6e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-08
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	7e-08
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	7e-08
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	8e-08
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-07
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-07
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-07
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	6e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	6e-07
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	6e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	6e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	7e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	8e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	9e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-06
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-06
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-06
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-06
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	4e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	7e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	7e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-05
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	2e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	6e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	7e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	8e-05
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	9e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-04
smart00360	73	smart00360, RRM, RNA recognition motif	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	2e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-04
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	3e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	3e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	4e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	6e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	6e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	7e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	8e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	8e-04
cd12301	74	cd12301, RRM1_2_PAR10_like, RNA recognition motif	8e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	8e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	9e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.001
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	0.001
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.001
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.001
cd12546	77	cd12546, RRM_RBM43, RNA recognition motif in verte	0.001
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.001
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.002
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.002
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.002
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.002
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.002
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.002
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.002
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.002
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.002
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	0.002
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	0.002
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.002
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.002
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.002
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.003
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.003
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.003
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.003
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.003
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.003
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.003
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.003
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.003
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.003
cd12624	91	cd12624, RRM_PRC, RNA recognition motif in peroxis	0.003
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.004
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.004
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.004
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.004
cd12492	85	cd12492, RRM2_RBM46, RNA recognition motif 2 found	0.004
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.004

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score =  100 bits (251), Expect = 8e-28
 Identities = 35/73 (47%), Positives = 47/73 (64%), Gaps = 2/73 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           +K+FVGRL ++ T EDLR+YFS+FG + DVY+PK    R F FVTFA+  VA  +    H
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPK--PFRAFAFVTFADPEVAQSLCGEDH 58

Query: 162 EICGQQVAIDSAT 174
            I G  V + +A 
Sbjct: 59  IIKGVSVHVSNAE 71

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 73.9 bits (182), Expect = 2e-17
 Identities = 37/81 (45%), Positives = 48/81 (59%), Gaps = 8/81 (9%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV-----PKRTGHRGFGFVTFAEEVVADR 155
            KKIFVG LP   T  DLR+YFS+FG + +V V      KR   RGFGF+TF  E   D+
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRP--RGFGFITFESEDSVDQ 59

Query: 156 V-SRRSHEICGQQVAIDSATP 175
           V +   H+I G++V +  A P
Sbjct: 60  VVNEHFHDINGKKVEVKRAEP 80

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

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

 Score = 69.2 bits (170), Expect = 1e-15
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV--S 157
            +FVG LP + T E+LR  FS+FG++  V +   K TG  +GF FV F  E  A++   +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 158 RRSHEICGQQV 168
               E+ G+ +
Sbjct: 61  LNGKELDGRPL 71

Length = 73

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

 Score = 68.8 bits (169), Expect = 1e-15
 Identities = 28/69 (40%), Positives = 44/69 (63%), Gaps = 4/69 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGH-RGFGFVTFAEEVVADRV-SRR 159
           +F+G L  + T E LR YFS++G ++D  + K   TG  RGFGFVTFA+    D+V + +
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 160 SHEICGQQV 168
            H + G+++
Sbjct: 61  PHVLDGREI 69

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 68.6 bits (168), Expect = 2e-15
 Identities = 34/75 (45%), Positives = 46/75 (61%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFAEEVVADRV-SR 158
           KIFVG LP + T E+ + YFS+FG+++D  +     TG  RGFGFVTF  E   +RV S 
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 159 RSHEICGQQVAIDSA 173
              E+ G+QV +  A
Sbjct: 61  GMLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

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

 Score = 66.2 bits (162), Expect = 1e-14
 Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTF-AEEVVADRVSR 158
           KIFVG L  E T E +R YF +FG I+++ +P   K    RGF F+TF +EE V   +  
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 159 RSHEICGQQVAIDSA 173
           + H I G++V +  A
Sbjct: 61  QFHVIGGKKVEVKKA 75

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 66.3 bits (162), Expect = 1e-14
 Identities = 33/70 (47%), Positives = 44/70 (62%), Gaps = 4/70 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRV-SR 158
           KIFVG L    T +D+++YFS+FG++ D  +   K+T  HRGFGFVTF  E V D+V   
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 159 RSHEICGQQV 168
             HEI  + V
Sbjct: 61  HFHEINNKMV 70

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 62.7 bits (153), Expect = 2e-13
 Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGHRGFGFVTFAEEVVADRV 156
           +FVG LP + T EDLR  FS+FG I  V + +      +GF FV F     A++ 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKA 55

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 62.2 bits (152), Expect = 4e-13
 Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADR 155
           +FVG LP + T EDL+  FS+FG I  + + +  TG  +GF FV F +E  A++
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEK 54

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

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 25/56 (44%), Positives = 38/56 (67%), Gaps = 2/56 (3%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTG-HRGFGFVTFAEEVVADRV 156
           +IFVG +P + T E+LR +FSRFG + DV  +  R G  +G+GFVTF  +  A+++
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKI 59

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 59.9 bits (146), Expect = 3e-12
 Identities = 28/57 (49%), Positives = 38/57 (66%), Gaps = 3/57 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADR 155
            KIFVG LP   T + LR+YFS+FG I +  V   ++TG  RG+GFVTF ++  A+R
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAER 57

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

 Score = 57.7 bits (140), Expect = 2e-11
 Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHR-GFGFVTFAEEVVADR-VSRRSH 161
           IFVG+L  + T E+L   FSR G+IL+V + KR  H   F F+ F  E  A R V   +H
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65

Query: 162 EI-CGQQV 168
            +   + +
Sbjct: 66  SMLKNKTM 73

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|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 = 57.6 bits (140), Expect = 2e-11
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 3/56 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADR 155
           K+FVG+LP+ AT ED+R  F  +G I +V +   K TG  +G  FV F+    A +
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQK 56

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

 Score = 57.2 bits (139), Expect = 3e-11
 Identities = 30/79 (37%), Positives = 42/79 (53%), Gaps = 5/79 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVS 157
           G K+FV  L    T ++L   FS+FGR+ +V + K   TG  RGFGFVTF     AD   
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 158 RR--SHEICGQQVAIDSAT 174
           R     E+ G+ + ++ A 
Sbjct: 61  RDLNGKELEGRVIKVEKAK 79

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

 Score = 57.1 bits (138), Expect = 3e-11
 Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEV-VADRVSR 158
           K+FVG L  E T E LRRYFS++G ++D  +         RGFGFV F +   V   ++ 
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 159 RSHEICGQQVAIDSATP 175
             H + G+ +     TP
Sbjct: 61  GPHTLDGRTIDPKPCTP 77

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

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

 Score = 56.8 bits (138), Expect = 4e-11
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGHRGFGFVTFAEEVVADRV--SRRS 160
           ++V  LP   T EDLR +FS +G++  V + + +   RGF FV FA    A+        
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 161 HEICGQQV 168
             + G+ +
Sbjct: 61  LVLDGRTL 68

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

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

 Score = 56.6 bits (137), Expect = 5e-11
 Identities = 31/77 (40%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SR 158
           K+F+G L  E T + L+ YFS++G I D  V   P     RGFGFVTFA     D   + 
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 159 RSHEICGQQVAIDSATP 175
           R H++ G++V    A P
Sbjct: 61  RPHKVDGREVEPKRAVP 77

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

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

 Score = 56.6 bits (137), Expect = 5e-11
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 3/62 (4%)

Query: 109 LPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVSRRSHEICG 165
           LP + T +DL+ YFS FG +L V V K  +TG  +GFGFV FA+     +V  + H I G
Sbjct: 7   LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMIDG 66

Query: 166 QQ 167
           + 
Sbjct: 67  RW 68

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

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

 Score = 56.1 bits (136), Expect = 7e-11
 Identities = 31/70 (44%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADR-VSR 158
           K+FVG L ++ T EDLR YFS++G +  V +   K TG  RGF FVTF +    D+ V +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 159 RSHEICGQQV 168
           + H I G +V
Sbjct: 61  KYHTINGHRV 70

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 56.2 bits (136), Expect = 7e-11
 Identities = 22/51 (43%), Positives = 34/51 (66%), Gaps = 3/51 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEE 150
           K+FVG LP    +++L+ YFS+FG++    VP  K TG  +G+GFV+F+  
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51

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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 56.2 bits (135), Expect = 7e-11
 Identities = 31/70 (44%), Positives = 42/70 (60%), Gaps = 4/70 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR- 158
           KIFVG L    T ED+++YF +FG++ D  +   K T  HRGFGFVTF  E + ++V   
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 159 RSHEICGQQV 168
             HEI  + V
Sbjct: 61  HFHEINNKMV 70

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>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 = 56.0 bits (136), Expect = 8e-11
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 3/57 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRVS 157
           +++G LP      +LR+YFS+FG +  + +   K+TG  +G+ FV F    VA  V+
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVA 58

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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 33/76 (43%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR 158
           KKIFVG L      ED+++YF +FG++ D  +   K T  HRGFGFVTF  E V ++V  
Sbjct: 4   KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

Query: 159 -RSHEICGQQVAIDSA 173
              HEI  + V    A
Sbjct: 64  IHFHEINNKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 55.0 bits (133), Expect = 2e-10
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-- 158
           ++ V  LP + T  DL++ FS FG + +V +P K  G  +GF FV F  +  A++  +  
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 159 RSHEICGQQVAIDSA 173
              +I G+ VA+D A
Sbjct: 61  NGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

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

 Score = 54.6 bits (131), Expect = 4e-10
 Identities = 32/76 (42%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-S 157
           KKIFVG L  EAT E +R YF  FG I  + +   PK    RGF F+TF EE    +V  
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

Query: 158 RRSHEICGQQVAIDSA 173
           ++ H + G +  I  A
Sbjct: 65  KKFHNVSGSKCEIKVA 80

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

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

 Score = 53.8 bits (130), Expect = 5e-10
 Identities = 25/55 (45%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVTFAEEVVADR 155
           +FV  LP + T E L  +FS  G I   +V K  G    RGFG+VTFA E  A R
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKR 56

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|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 = 53.8 bits (130), Expect = 7e-10
 Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRT--GHRGFGFVTFA 148
            K+ V  +P EAT ++LR  FS FG++  V +PK+    HRGF FV F 
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFV 49

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

 Score = 52.9 bits (127), Expect = 1e-09
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADR-V 156
             K+FVG L  + +   LRR+F+R+G++ +  V   P     RGFGF+TF+    AD  +
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 157 SRRSHEICGQQVAIDSA 173
             + H I G Q+ +  A
Sbjct: 62  EAQPHSIDGNQIELKRA 78

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

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 52.3 bits (126), Expect = 2e-09
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRAT 45
          +PK       R   F+TFA  +  ++L  + H + G +V V  A 
Sbjct: 32 IPKP-----FRAFAFVTFADPEVAQSLCGEDHIIKGVSVHVSNAE 71

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVTFAEE 150
           ++VG L +E   + L   F  FG I D+ +P       HRGF FV F E 
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP 50

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

 Score = 52.0 bits (125), Expect = 3e-09
 Identities = 29/69 (42%), Positives = 43/69 (62%), Gaps = 4/69 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SRR 159
           +F+G L  + TAE LR YFS+FG I +  V   P     RGFGFVTF++    D+V ++ 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 160 SHEICGQQV 168
            HE+ G+++
Sbjct: 61  PHELDGKKI 69

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

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

 Score = 51.6 bits (124), Expect = 4e-09
 Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 8/61 (13%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV-PKRTGHR--GFGFVTF-----AEEVVAD 154
           ++FVG LP + T ++L+ +F  FG +L+V +  K  G R   FGFV F      ++++A+
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 155 R 155
           +
Sbjct: 65  K 65

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 55.0 bits (131), Expect = 5e-09
 Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR 158
             +FVG LP + T EDLR  F +FG +  V +   + TG  RGF FV F  E  A++   
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 159 RSH--EICGQQVAIDSATPLDD 178
             +  E+ G+ + +  A P   
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQ 197

Length = 306

>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 = 51.1 bits (123), Expect = 6e-09
 Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR--VSRRSH 161
           ++VG LP   T E+L+R FS FG I +V V K    +G+ FV F     A    V+    
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD---KGYAFVRFDTHEAAATAIVAVNGT 59

Query: 162 EICGQQV 168
            I GQ V
Sbjct: 60  SINGQTV 66

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

>gnl|CDD|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 = 50.8 bits (122), Expect = 7e-09
 Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 3/48 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTF 147
           ++FV  LP   T E+LR  F  FG I +V++P  K T   +GF FV+F
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSF 48

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

 Score = 50.6 bits (121), Expect = 8e-09
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHE 162
           K+FVG LP EAT +++R  F ++G++L+  + K      +GFV   ++  AD   R  H 
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIK-----NYGFVHMDDKTAADEAIRNLHH 56

Query: 163 ICGQQVAID 171
                VAI+
Sbjct: 57  YKLHGVAIN 65

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

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

 Score = 50.2 bits (121), Expect = 1e-08
 Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVSRR 159
           V  L ++A  +DLR  F  FG I  VY+ K   TG  RGF FVTF     A+R   +
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

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

 Score = 50.3 bits (120), Expect = 1e-08
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVSRRS 160
           +F+G L  E T + LR YF +FG + D  V +   TG  RGFGF+TF +    + V ++ 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 161 HEICGQQVAIDSATP 175
           H + G+ +    A P
Sbjct: 61  HILDGKIIDPKRAIP 75

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

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 3/76 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTGHRGFGFVTFAEEVVADRVSRRS 160
           K++ V  +P      DLR+ F +FG ILDV  +    G +GFGFVTFA    ADR   + 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 161 HE--ICGQQVAIDSAT 174
           H   + G+++ +++AT
Sbjct: 61  HGTVVEGRKIEVNNAT 76

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 50.3 bits (120), Expect = 1e-08
 Identities = 30/80 (37%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSR 158
           K+FVG L  +    DL  +FS+FG +   +V   K+TG  RGFGFV F     AD+    
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 159 RSHEICGQQVAIDSATPLDD 178
           + H I G +V +  A P ++
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

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

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFA-EEVVADRVSR 158
           K+FVG L  + T E ++ YF  FG I ++ +P   K    RGF FVT+  EE V   +  
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 159 RSHEICGQQVAIDSA 173
           R H+I   +  I  A
Sbjct: 61  RYHQIGSGKCEIKVA 75

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRT--GHRGFGFVTFAEEVVADRVSRRS- 160
           +FVG L   A  +DL  +F   G ++DV + +      +GFG V FA E  A +   +S 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSG 61

Query: 161 HEICGQQVAIDSATP 175
            E+ G+++ +D AT 
Sbjct: 62  EELLGREIRVDLATE 76

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

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 24/49 (48%), Positives = 30/49 (61%), Gaps = 4/49 (8%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG----HRGFGFVTF 147
           KI V  +P EAT ++LR  FS FG +  V +PK+      HRGFGFV F
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDF 50

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

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVTF 147
           +FVG L    T  DL   FSRFG + DV + K+      RGF ++  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL 48

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VS 157
           KKIFVG + ++     LR YF ++G+I  ++V   +++G  RGF FVTF +    D+ V 
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60

Query: 158 RRSHEICGQQVAIDSATP 175
           ++ H I G    +  A  
Sbjct: 61  QKYHTINGHNCEVKKALS 78

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADRV 156
            ++VG LP   T EDL+  F +FG +    V   + TG  RGFGFV       A+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57

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

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV 156
           I+VG++P + T  +LR+ F  FG I ++ +  R     +GFVT+     A R 
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRA 57

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

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

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 6/53 (11%)

Query: 103 KIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
           ++FVG L   + + EDL   FS++G+IL + +     H+G+GFV F  E  A 
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL-----HKGYGFVQFDNEEDAR 49

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

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

 Score = 48.8 bits (116), Expect = 5e-08
 Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SR 158
           K+F+G L  + T E LR YF +FG + +  V   P     RGFGFVTF ++   D+V ++
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 159 RSHEI 163
             HE+
Sbjct: 62  SRHEL 66

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

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

 Score = 48.5 bits (115), Expect = 6e-08
 Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRR 159
           K+F+G L  + + + LR YFS+FG I +  V   P     RGFGFVTFA+    D+V  +
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 160 SH 161
            H
Sbjct: 61  PH 62

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

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

 Score = 48.0 bits (115), Expect = 6e-08
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR--S 160
           K++VG L   AT  +L   F ++G +  V+V +     GF FV F +   A+   R    
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP--GFAFVEFEDPRDAEDAVRALDG 58

Query: 161 HEICGQQVAIDSATP 175
             ICG +V ++ +  
Sbjct: 59  RRICGNRVRVELSRG 73

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

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

 Score = 48.0 bits (115), Expect = 7e-08
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 5/53 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           K+FVG LP   T+E+LR  F ++G + +  V K      +GFV   EE  A+ 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN-----YGFVHMEEEEDAED 48

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

 Score = 48.1 bits (115), Expect = 7e-08
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADR--VSR 158
           IFVG L  E   E LR  F+ FG I D  V K  +TG  +G+GFV+F ++  A+    S 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 159 RSHEICGQQV 168
               + G+ +
Sbjct: 62  NGQWLGGRAI 71

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

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 47.9 bits (114), Expect = 7e-08
 Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 4/67 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SRR 159
           +FVG L  + T +DL+ YFS+FG ++D  +   P     RGFGFV F +    ++V  ++
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 160 SHEICGQ 166
            H++ G+
Sbjct: 61  EHKLDGR 67

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 48.1 bits (114), Expect = 7e-08
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SRR 159
           +F+G L  + T +DL+ YFS+FG ++D  +   P     RGFGFV F E    D+V  ++
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 160 SHEICGQQV 168
            H++ G+ +
Sbjct: 61  EHKLNGKVI 69

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>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 = 48.2 bits (115), Expect = 8e-08
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSRR 159
           K+FVG++P+    +DLR  F +FG+I ++ V   K TG H+G  F+T+     A +    
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 160 SHE 162
            HE
Sbjct: 67  LHE 69

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

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SR 158
           K+FVG L  + + +DL+ YF++FG + D  +   P     RGFGF+ F +    ++V  +
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 159 RSHEICGQQV 168
           + H + G+ +
Sbjct: 61  KEHRLDGRLI 70

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

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

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVTFAEEVVADRVSRRSHE 162
           V  L    T +DLRR F ++G + DVY+P+       RGF FV F ++  A+        
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

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

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTGH-RGFGFVTFAEEVVADR-VS 157
           KKIFVG + ++     LR YF ++G+I  +++   + +G  RGF FVTF +    D+ V 
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60

Query: 158 RRSHEICGQQVAIDSA 173
           ++ H + G    +  A
Sbjct: 61  QKYHTVNGHNCEVRKA 76

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

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 16/43 (37%), Positives = 29/43 (67%), Gaps = 3/43 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFV 145
           ++FVG LP + T E+ +  FS++G + +V++ K    +GFGF+
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE---KGFGFI 42

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

 Score = 46.6 bits (111), Expect = 3e-07
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 13/81 (16%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRVSR 158
             ++V  +      +DLRR F ++G I+DVY+P    T   RGF +V F  E V D  + 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQF--EDVRD--AE 56

Query: 159 RSH------EICGQQVAIDSA 173
            +          G+++ I  A
Sbjct: 57  DALYYLDRTRFLGREIEIQFA 77

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 46.1 bits (109), Expect = 4e-07
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SR 158
           K+F+G L  + + +DL  Y SRFG +LD  +   P     RGFGFV F +    D+V   
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 159 RSHEICGQQV 168
           + H++ G+ +
Sbjct: 61  KEHKLDGKLI 70

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 46.0 bits (109), Expect = 5e-07
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSR-- 158
           +FV  L    T EDL  +FS    I    V   P+    RG+GFVTFA    A       
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 159 RSHEICGQQVAIDSATP 175
           ++ ++ G+ + +D A  
Sbjct: 62  KNKKLHGRILRLDIAER 78

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

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 7/73 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH- 161
           ++++GRLP  A   D+ R+F  +GRI ++ +       GFGFV F +   AD      + 
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL-----KNGFGFVEFEDPRDADDAVYELNG 55

Query: 162 -EICGQQVAIDSA 173
            E+CG++V ++ A
Sbjct: 56  KELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 45.5 bits (108), Expect = 6e-07
 Identities = 26/57 (45%), Positives = 34/57 (59%), Gaps = 3/57 (5%)

Query: 114 TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFA-EEVVADRVSRRS-HEICGQQV 168
           T ED+  YF +FG +LDV +P     R FGFVTF   E V   +S+ + H ICG +V
Sbjct: 12  TEEDVSEYFGQFGPVLDVRIP-YQQKRMFGFVTFENAETVKRILSKGNPHFICGSRV 67

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

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

 Score = 45.6 bits (108), Expect = 6e-07
 Identities = 23/47 (48%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGHRGFGFVTF 147
           KI V  LP EAT +D+R  FS +G++  V VPK+     RGF FV F
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEF 48

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

 Score = 45.9 bits (108), Expect = 6e-07
 Identities = 28/71 (39%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVAD-RVS 157
           +K+F+G L  E T E LR Y+ ++G++ D  V   P     RGFGFVTF+     D  ++
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 158 RRSHEICGQQV 168
            R H I G+ V
Sbjct: 63  ARPHTIDGRVV 73

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

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

 Score = 45.7 bits (108), Expect = 6e-07
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGHR-GFGFVTFAEEVVADRVSRR 159
           K+FVG +P+  T +++R  F   G +L+V +   KRTGH+ G  FV ++    ADR  R 
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 160 SH 161
            H
Sbjct: 61  LH 62

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

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

 Score = 45.3 bits (108), Expect = 7e-07
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTGH-RGFGFVTFAEEVVADRV 156
           + +F+  LP +AT E+L+  FS+FG +    +   K TGH +G  FV F  +  A + 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKC 58

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

 Score = 45.3 bits (108), Expect = 8e-07
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 6/59 (10%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG------HRGFGFVTFAEEVVADR 155
           +I+V  L  +   +DLR  FS+FG +  + +PK+        + GF FVTF +   A+ 
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

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

 Score = 45.2 bits (108), Expect = 8e-07
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)

Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAE 149
           +++  L ++   ++L+R     FS+FG +LD+   K    RG  FV F +
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKD 51

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

 Score = 45.0 bits (107), Expect = 9e-07
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTGHRGFGFVTFAE 149
           ++V  LP+ AT E L+  FS++G ++ V +P+       +GF F+ F  
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFET 50

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEE 150
           K +FV RL  + T   LRR F  +G I  + +   K+TG  RG+ F+ F  E
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHE 53

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

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VS 157
           KK+FVG + ++     LR YF  +G+I  +++   +++G  RGFGFVTF +    D+ V 
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 158 RRSHEICGQQVAIDSA 173
           ++ H I G    +  A
Sbjct: 61  QKYHTINGHNAEVRKA 76

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 16/52 (30%), Positives = 33/52 (63%), Gaps = 3/52 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
           ++FVG LP + T E++R+ F ++G+  ++++ K    +GFGF+      +A+
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHK---DKGFGFIRLETRTLAE 51

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 44.2 bits (104), Expect = 2e-06
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 3/51 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEE 150
           KIFVG L  +   E +R YF  FG +  + +P   K    RGF F+TF EE
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEE 51

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

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

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 6/72 (8%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T + LR +F ++G + D  V   P+    RGFGFVT++  EEV A   
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 157 SRRSHEICGQQV 168
           + R H++ G+ V
Sbjct: 63  A-RPHKVDGRVV 73

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

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

 Score = 43.9 bits (103), Expect = 3e-06
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAE-EVVADRVS 157
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT++  E V   ++
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 158 RRSHEICGQQV 168
            R H++ G+ V
Sbjct: 63  ARPHKVDGRVV 73

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

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 3/47 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTF 147
           +F+  LP E T +DL + F+ FG ++   V+V K TG  + FGFV++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSY 47

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

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 2/67 (2%)

Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTG-HRGFGFVTFAEEVVADRVS 157
           I  +IFVG +  +    DLR++FS++G + +V  V  R G  +G+GFVTF  +  A ++ 
Sbjct: 1   IPNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKIL 60

Query: 158 RRSHEIC 164
           + ++ +C
Sbjct: 61  QEANRLC 67

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAE 149
            ++FV  LP     +DL + FS+FG + +V+V   K++G  +GF +V F +
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLD 53

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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 43.0 bits (101), Expect = 4e-06
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR--S 160
           ++F+GRL   A  +D+ R+F  +GRI D+ +      RGFGFV F +   AD        
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDL-----KRGFGFVEFDDPRDADDAVYELDG 55

Query: 161 HEICGQQVAIDSA 173
            E+C ++V I+ A
Sbjct: 56  KELCNERVTIEHA 68

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|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 = 43.3 bits (102), Expect = 4e-06
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTGHRGFGFVTFAEEVVADRVSRR 159
           K+F+G L  +   + L + FS++G+I +V V K       RGFGFVTF     A      
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 160 --SHEICGQQVAIDSA 173
                + G+Q+ +D A
Sbjct: 62  MNGKSVDGRQIRVDQA 77

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

 Score = 42.6 bits (100), Expect = 7e-06
 Identities = 29/77 (37%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP-----KRTGHRGFGFVTFAEEVVADRVSR 158
           +FV  +  +  +EDLRR F R+G I+DVYVP     +R   RGF +V F +   A+    
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRP--RGFAYVQFEDVRDAEDALH 60

Query: 159 RSHE--ICGQQVAIDSA 173
                 ICG+Q+ I  A
Sbjct: 61  NLDRKWICGRQIEIQFA 77

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

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

 Score = 42.4 bits (100), Expect = 7e-06
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAE 149
           + +F+G L +  T  DLR  F RFG I+D+ + K+ G+  + F+ +A+
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYAD 50

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

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGH-RGFGFVTFAEEVVADRVSR 158
             +FVGRL  + T E LR  FSR+G I  + + +   TG  +G+ FV +  E  A R  R
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 159 RSHE--ICGQQVAID 171
            +H+  I G ++ +D
Sbjct: 64  DAHKLVIDGSEIFVD 78

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPK 47
          KD  +K  RG GF+TFASA  V+  M    H++ G  V   RA P+
Sbjct: 33 KDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGREVEPKRAVPR 78

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

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

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 4  DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATP 46
          D   K  RG GFITF S DSV+ ++ +  H++ G  V V RA P
Sbjct: 37 DHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGKKVEVKRAEP 80

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

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

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR--S 160
           KIFVG + ++ + E+LR  F  +G +L   V ++     F FV    E  ADR       
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-----FAFVHLRGEAAADRAIEELNG 56

Query: 161 HEICGQQVAID 171
            E+ G+++ ++
Sbjct: 57  RELHGRKLVVE 67

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

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAE 149
           ++VG L    T +DLR  F  FG I  V + +   TG  +G+GF+ FA+
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFAD 49

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

 Score = 44.9 bits (106), Expect = 2e-05
 Identities = 44/209 (21%), Positives = 76/209 (36%), Gaps = 43/209 (20%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
             KD+ S+  +G+ ++ F   +SV   +  T ++     ++ +++  E +          
Sbjct: 121 CIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKN---------- 170

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
                        R A        D P               K++VG L    T ++LR+
Sbjct: 171 -------------RAAKAATHQPGDIPNF------------LKLYVGNLHFNITEQELRQ 205

Query: 121 YFSRFGRILDVYVPK--RTGH-RGFGFVTF--AEEVVADRVSRRSHEICGQQVAIDSA-- 173
            F  FG I DV + +   TG  +GFGF+ F  AEE           E+ G+ + +  A  
Sbjct: 206 IFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD 265

Query: 174 -TPLDDAGPSQNFMMNAAETFGGYGGPMR 201
            T L DA  +   +    +         R
Sbjct: 266 STYLLDAANTFEDIDKQQQMGKNLNTEER 294

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|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           +FVG L    T ++LR  F  FG I+ V +P     +G GFV F     A+ 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP---GKGCGFVQFVHRAAAEA 52

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
           ++FVG LP + T ED ++ F ++G   +V++ +    RGFGF+      +A+
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINR---DRGFGFIRLESRTLAE 51

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGHRGFGFVTFAEEVVADR 155
           +FVG L    T E+LRR F R+G + DV +  P R     + FV F    +A R
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHR 58

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

>gnl|CDD|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 = 41.1 bits (97), Expect = 2e-05
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRF-GRILDVYV--PKRTGHRGFGFVTFAEE 150
           ++ V  LP   T  +L+ +FS+  G I DV +   +    R   F+ +  E
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTE 52

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 118 LRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHE--ICGQQVAID 171
           L + FS FG +  + + K+    GF FV F+ E  A++  +  +     G+ + +D
Sbjct: 1   LYKLFSPFGNVEKIKLLKK--KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

(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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 33/108 (30%), Positives = 49/108 (45%), Gaps = 5/108 (4%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFAEEVV 152
           S + +  K+F+G L        LR  F+ FG ++D  V V + TG  RGFGFV F +E  
Sbjct: 29  SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGA 88

Query: 153 ADRVSRR--SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGG 198
           A          E+ G+ + ++ A     A  +       +   GGYGG
Sbjct: 89  ATAAISEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGG 136

Length = 144

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 114 TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSA 173
           + ++LR+ FS++G + DV V  +   +G   V FA +  A+         CG       +
Sbjct: 17  SEDELRKIFSKYGDVSDVVVSSK--KKGSAIVEFASKKAAEAA---VENECG-----LPS 66

Query: 174 TPLD 177
            PL 
Sbjct: 67  NPLL 70

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|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 = 40.9 bits (96), Expect = 3e-05
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 7/76 (9%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGH-RGFGFVTFAEEVVADRVSR- 158
           +FVG +P EAT E L+  FS  G ++    VY  + TG  +G+GF  + ++  A    R 
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY-DRETGKPKGYGFCEYKDQETALSAMRN 59

Query: 159 -RSHEICGQQVAIDSA 173
              +E+ G+Q+ +D+A
Sbjct: 60  LNGYELNGRQLRVDNA 75

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

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 7/50 (14%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-----KRTGHRGFGFVTF 147
           ++F+  L    T EDL + FS++G + +V++P     K+   +GF FVT+
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP--KGFAFVTY 51

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

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 3/50 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEE 150
           +FVG L  E T ++LR +F R GRI  V +   + +G  +GF FV F E 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEI 50

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

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 2/62 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFAEEVVADRVSRRSH 161
           +FV  L      ++LR+ FS+ G I DV + K      +G+ +V F  E       +   
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDR 61

Query: 162 EI 163
           E+
Sbjct: 62  EL 63

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

 Score = 39.8 bits (93), Expect = 6e-05
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 3/58 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRVSR 158
           I++G LP     ++L++YFS+FG + +V V   K+TG+ + +GF+ F    VA   ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK 59

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

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 23/49 (46%), Positives = 27/49 (55%), Gaps = 5/49 (10%)

Query: 114 TAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSRR 159
           T  DLR  FSR+G I  V V   ++TG  RGFGFV F  E V D    +
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYF--ESVEDAKEAK 58

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

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFV--TFAEEVVADRVSRRS 160
           KIFVG +    T+++LR  F  FGR+++    K      + FV     EE +A   +   
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKVK-----DYAFVHMEREEEALAAIEALNG 56

Query: 161 HEICGQQVAID 171
            E+ G+++ ++
Sbjct: 57  KEVKGRRINVE 67

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

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

 Score = 42.6 bits (99), Expect = 8e-05
 Identities = 30/165 (18%), Positives = 48/165 (29%), Gaps = 29/165 (17%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           + +D+ +   RG  F+ F S +S E     ++  EL G  + V +A P     R     +
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP-RSELSNN 205

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                A       A                               ++VG LP +   E+L
Sbjct: 206 LDASFAKKLSRGKALLLEK-----------------------SDNLYVGNLPLKTAEEEL 242

Query: 119 RRYFSRFGRILDV---YVPKRTGHRGFGFVTFAEEVVADRVSRRS 160
              F   G I+             +   FV       A   + R 
Sbjct: 243 ADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRG 287

Length = 306

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 39.5 bits (92), Expect = 8e-05
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 7/73 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV--SRRS 160
           ++++GRL      +D++R+F  +G++L++ +       G+GFV F +   AD        
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL-----KNGYGFVEFEDSRDADDAVYELNG 55

Query: 161 HEICGQQVAIDSA 173
            ++CG++V ++ A
Sbjct: 56  KDLCGERVIVEHA 68

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           K +FVG LP+ AT E +R  F + G I+ +    R   + F  + FAEE   D+    S 
Sbjct: 7   KTVFVGGLPENATEEIIREVFEQCGEIIAI----RMSKKNFCHIRFAEEFAVDKAIYLS- 61

Query: 162 EICGQQVAIDSATPLDDAG 180
              G +V I S+T   ++G
Sbjct: 62  ---GYRVRIGSSTDPKNSG 77

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

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

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 4/54 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH---RGFGFVTFAEEVVA 153
           K+FVG L ++AT +++   FS +GR+ D+Y+  R      RG  FV ++ + +A
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYM-MRDEMKQSRGCAFVKYSSKEMA 53

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTGH-RGFGFVTFAEEVVADR 155
            K+FV  LP   T E+L + F + G +  V  V  R+G  +G  +V +  E  A +
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQ 58

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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAE 149
           +IFVG L  E T E L R FS++       V   KRTG  +G+GFV+F++
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFA 148
           + VG LP E T E  R   S FG +   ++   + TG  +G+GFV +A
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYA 49

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

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADR 155
           V  LPQ+ T E+LR  F   G I    +   + TG   G+GFV + +E  A +
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQK 57

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|214636 smart00360, RRM, RNA recognition motif

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVV 41
          + +D+ +   +G  F+ F S +  E  +  ++  EL G  + V
Sbjct: 31 LVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
          KD+GSK  RG G++TFA  +  +  +      + GG  + V+ A  K
Sbjct: 33 KDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKKK 79

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTGHRGFGFVTFAEEVV 152
           E  QR  + +F+G L    T  DLRR F RFG I  +D+  P R     +GF+ F    +
Sbjct: 1   EDDQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDM 60

Query: 153 ADR 155
           A R
Sbjct: 61  AHR 63

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|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 = 38.8 bits (91), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGHRGFGFVTFAEEVVADRVSRR- 159
           +FVG +P +AT E L   FS  G ++    V        +G+GF  F +   A    R  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 160 -SHEICGQQVAIDSA 173
             +E  G+ + +D A
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFGFVTF 147
           G  +F+  LPQE T  DL + F  FG ++   V++ K+T   + FGFV++
Sbjct: 4   GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSY 53

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDV--YVPKRTGH-RGFGFVTFAEEVVA 153
           +++  LP   T EDL +    FG+I+     + K+T   +G+GFV F     A
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAA 55

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV--YVPKRTG-HRGFGFVTFAEEVVAD 154
           +I+V  +  + + +D++  F  FG+I          TG H+G+GF+ +     A 
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQ 56

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV-PKRTGH-RGFGFVTFAEEVVADR 155
           +I V  LP+  T + LR +F   G + DV V   R G  R FGFV F  E  A +
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQ 56

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTGHRGFGFVTFAEEVVAD 154
           ++VG L ++ T E L   F + G +++V++PK      H+G+GFV F  E  AD
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDAD 54

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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 4/50 (8%)

Query: 102 KKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE 150
             + V  +P E      L  +FS+FG I+++ V           V F+  
Sbjct: 2   TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYN-PES--ALVQFSTS 48

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV--SRRS 160
           ++++GRL  +A   D+ R+F  +G+IL+V +       G+GFV F +   AD        
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDL-----KNGYGFVEFDDLRDADDAVYELNG 55

Query: 161 HEICGQQVAID 171
            ++CG++V ++
Sbjct: 56  KDLCGERVIVE 66

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADR 155
           IFVG L  E T   L   FS F    D  V    ++G  RG+GFV+F  +  A+ 
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAEN 56

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

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRIL--DVYVPKRTGHR-GFGFVTFAEEVVADR 155
           +FV +L    T EDL   FSRFG+I   +V   K+TG    + F+ F  +   + 
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 4/65 (6%)

Query: 105 FVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH-RGFGFVTFAEEVVADRVSRRSH-- 161
            V  LP E + +D       FG    V V  R G  +   F TF  E  A +   R H  
Sbjct: 3   LVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQL 61

Query: 162 EICGQ 166
           +I G+
Sbjct: 62  KILGK 66

This subfamily corresponds to the RRM1 of 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 repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), 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. . Length = 73

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

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEV 151
           +FVG LP +   E+LR++F   G +  V +    K    +GFG+V F  + 
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKD 52

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

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADR--VSR 158
           +FVG L  E T ED++  F+ FG+I D  V K   TG  +G+GFV+F  ++ A+   V  
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 159 RSHEICGQQVAIDSAT 174
               + G+Q+  + AT
Sbjct: 64  GGQWLGGRQIRTNWAT 79

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRT-GHRGFGFVTFAEEVVADRVSRRS 160
           ++V  L     A DL++ FS++G+++   +    R+ G R FGFVT A    A +  +  
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 161 H--EICGQQVAID 171
           H  E+ G+ ++++
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP-----KRTGHRGFGFVTFAEEVVADRV-- 156
           +FV  +      EDLRR F R+G I+DVYVP     +R   RGF ++ F +   A+    
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRP--RGFAYIQFEDVRDAEDALY 60

Query: 157 SRRSHEICGQQVAIDSA 173
           +     +CG+Q+ I  A
Sbjct: 61  NLNRKWVCGRQIEIQFA 77

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

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTF 147
           ++V  L ++   E L+  F ++G+I    V K   G  +GFGFV F
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNF 49

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

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 3/47 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTF 147
           +FVG LP + TAEDL  +F   G    V +   K+TG  +G  FV F
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEF 49

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

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
           ++ G  P      D++R F   G +  V +  RT  +   F+TF
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRT-VQPHAFITF 44

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

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFA 148
           + +++G LP+  + E+LR    +FG I  + + K    +   FV F 
Sbjct: 4   RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE---KNIAFVHFL 47

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

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

 Score = 40.2 bits (94), Expect = 6e-04
 Identities = 39/164 (23%), Positives = 55/164 (33%), Gaps = 32/164 (19%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
              GS   RG  F+ F   +     +  ++  ++G +         KE     VGR    
Sbjct: 211 MKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA---------KEGKKLYVGRAQ-- 259

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
                      A R A L     ++       +    +  G  ++V  L    T E LR 
Sbjct: 260 ---------KRAEREAELRR--KFEE----LQQERKMKAQGVNLYVKNLDDTVTDEKLRE 304

Query: 121 YFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRRSH 161
            FS  G I    V    K    RGFGFV F+    A+R     H
Sbjct: 305 LFSECGEITSAKVMLDEKGVS-RGFGFVCFSNPEEANRAVTEMH 347

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFA 148
           +K+FVG L ++    D+R  F+ FG I +  V +      RG  FVTFA
Sbjct: 2   RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFA 50

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

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADR 155
            +FVG L      E L+  F +FG ++   V   + TG  RGFG+V F     A +
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKK 56

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

 Score = 37.1 bits (87), Expect = 6e-04
 Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGHRGFGFVTFAEEVVADR 155
           IF+  L +    + L   FS FG IL   V      G +G+GFV F  E  A R
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVR 58

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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 37.1 bits (86), Expect = 7e-04
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 5/58 (8%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF-----AEEVVADR 155
           +I+VG LP +   +DL   F ++GRI D+ +  R G   F FV F     AE+ V  R
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGR 58

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 36.6 bits (85), Expect = 8e-04
 Identities = 15/52 (28%), Positives = 25/52 (48%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
           +I+VG LP +    D+   F ++G I  + +  R     F FV F +   A+
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAE 52

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

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

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 9/74 (12%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGH--RGFGFVTFAEEVVADRVSRRS 160
           + VG+L +    + L+  FS +G + DV +P  R  +  RG+ +V F  E   D      
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEF--ESPEDAEKAIK 58

Query: 161 H----EICGQQVAI 170
           H    +I GQ+V +
Sbjct: 59  HMDGGQIDGQEVTV 72

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

>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase PARP-10, RNA recognition motif 2 in PARP-14, RNA recognition motif in N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35), RNA-binding protein 43 (RBM43) and similar proteins

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 9/72 (12%)

Query: 103 KIFVGRLPQEATAEDLRRYF-----SRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV- 156
            + V  LP+  + + L  YF     S  G +  V   +  G      VTFA+  VA+RV 
Sbjct: 2   CVLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQYLREKGS---ALVTFADFKVAERVV 58

Query: 157 SRRSHEICGQQV 168
            ++ H + G Q+
Sbjct: 59  KQKKHPLNGTQL 70

This subfamily corresponds to the RRM1 and RRM2 of PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35) and RNA-binding protein 43 (RBM43). PARP-10 is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells. PARP-10 may also play a role in nuclear processes including the regulation of chromatin, gene transcription, and nuclear/cytoplasmic transport. PARP-10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM). PARP-14, also termed aggressive lymphoma protein 2, is a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. Like PARP-10, PARP-14 also includes two RRMs at the N-terminus. Nmi, also termed N-myc and STAT interactor, is an interferon inducible protein that interacts with c-Myc, N-Myc, Max and c-Fos, and other transcription factors containing bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc proteins, Nmi also associates with all the Stat family of transcription factors except Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can enhance Stat-mediated transcriptional activity through recruiting the Stat1 and Stat5 transcriptional coactivators, CREB-binding protein (CBP) and p300. IFP 35 is an interferon-induced leucine zipper protein that can specifically form homodimers. Distinct from known bZIP proteins, IFP 35 lacks a basic domain critical for DNA binding. In addition, IFP 35 may negatively regulate other bZIP transcription factors by protein-protein interaction. For instance, it can form heterodimers with B-ATF, a member of the AP1 transcription factor family. Both Nmi and IFP35 harbor one RRM. RBM43 is a putative RNA-binding protein containing one RRM, but its biological function remains unclear. . Length = 74

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

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGHRGFGFVTFAEEV 151
           +FVG L    T E L   F + G +  V +PK      + F FVTF  EV
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEV 53

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

 Score = 36.9 bits (85), Expect = 9e-04
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVS 157
           G +IFVG++P++   ++L   F + G I D+ +   P    +RG+ FVTF  +  A    
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

Query: 158 R--RSHEI 163
           +   +HEI
Sbjct: 61  KLYNNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 4  DQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA 44
          D  +   RG GF+TF S  +VE +      ELGG  V V RA
Sbjct: 34 DHDTGRSRGFGFVTFDSESAVERVFSAGMLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTV 39
          +D  +K  RG GF+TF+   SV+  L    HEL G  +
Sbjct: 32 RDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKI 69

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

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 5/75 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGH-RGFGFVTFAEEVVADRVSRRS 160
           IFV  + +EA  ED+   F+ FG I ++++   +RTG  +G+  + +  +  A       
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 161 H--EICGQQVAIDSA 173
           +  E+ GQ +++D A
Sbjct: 69  NGKELLGQTISVDWA 83

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

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 4/50 (8%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGF-G--FVTFAEE 150
           ++V   P++AT +D++ +F +FG++ ++ + +R   + F G  FV F  E
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRM-RRDLDKKFKGSVFVEFKTE 50

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240990 cd12546, RRM_RBM43, RNA recognition motif in vertebrate RNA-binding protein 43 (RBM43)

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 12/77 (15%)

Query: 102 KKIFVGRLP----QEATAEDLRRYFSR----FGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           + + V  LP      A  + L  +F R     G + +V  P RT   G  +VTF EE  A
Sbjct: 1   RTVVVSGLPDGVFDGALKDKLTIHFQRRKNGGGDVENVTYPTRTK--GVAYVTFEEEEDA 58

Query: 154 DRVSRRSH--EICGQQV 168
           + V ++ H  +     V
Sbjct: 59  ENVLKKKHVLQDKSLGV 75

This subgroup corresponds to the RRM of RBM43, a putative RNA-binding protein containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although its biological function remains unclear, RBM43 shows high sequence homology to poly [ADP-ribose] polymerase 10 (PARP-10), which is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. . Length = 77

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 4/55 (7%)

Query: 99  RIGKKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAE 149
           R    I++  L ++   ++L++     FSRFG+ILD+ V +    RG  FV F E
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 55

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 15/52 (28%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
           ++FVG LP + T ++ ++ F+++G   +V++ K    +GFGF+      +A+
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK---GKGFGFIKLESRALAE 51

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 4  DQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDR 43
          D+ +  HRG GF+TF S D V+ +  +  HE+    V   +
Sbjct: 34 DKQTNRHRGFGFVTFESEDVVDKVCEIHFHEINNKMVECKK 74

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGH-RGFGFVTFAEEVVADRV--SR 158
           +FVG L  +A  + +   F  +G I  V +P    +G  +GFG+V F+ +  A     + 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 159 RSHEICGQQVAID 171
              ++ G+ V +D
Sbjct: 61  GGTDLLGRPVRLD 73

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

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 7/58 (12%)

Query: 99  RIGKKIFV-GRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           R G  ++V G      T E L++ FS FG I+++ + K    +  GFVTF +   ADR
Sbjct: 2   RKGNTLYVHGY---GLTEEILKKAFSPFGNIINISMEK---EKNCGFVTFEKMESADR 53

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGHR-GFGFVTFAEEVVADR 155
           V  LPQ  T +++R  FS  G I    +   K TG   G+GFV + +   A++
Sbjct: 6   VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEK 58

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFAEEVVADRVSRR 159
           +K+F+G + ++    D+R  FS FG+I +  + +      RG  FVTF    +A    + 
Sbjct: 2   RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 61

Query: 160 SHE 162
            H+
Sbjct: 62  MHQ 64

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 5/86 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFGFVTFAEEVVADRV- 156
           G  +F+  LPQE   +DL + F  FG ++   V++ K+T   + FGFV++   V A    
Sbjct: 7   GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66

Query: 157 -SRRSHEICGQQVAIDSATPLDDAGP 181
            +    +I  +++ +      +D+ P
Sbjct: 67  QAMNGFQIGMKRLKVQLKRSKNDSKP 92

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

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 116 EDLRRYFSRFGRILDVYVPKRTGHR--GFGFVTFAEEVVADRV--SRRSHEICGQQVAID 171
             L++ F R+G++ +  +P++ G +  GF FVT  +   A+    +    EI G+ VA+D
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

Query: 172 SA 173
            A
Sbjct: 76  WA 77

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTF 147
           G  +F+  LPQE    +L + F  FG ++   V+V + T   + FGFV+F
Sbjct: 4   GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSF 53

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFGFVTF 147
           Y R  S    G  ++V  LP+  T  +L   FS FG+I+   +     TG  +G GF+ F
Sbjct: 79  YARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF 138

Query: 148 AEEVVADR 155
            +   ADR
Sbjct: 139 DKRDEADR 146

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|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 118 LRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQ 167
           L   F RFG ++DVY+      + +G+  +A+   A+R     H  E+ G +
Sbjct: 16  LEDVFCRFGGLIDVYL---VPGKNYGYAKYADRESAERAITTLHGKEVNGVK 64

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEE 150
           IFVG +    T E+L+ +F   G I  + +   K TG  +GF ++ F ++
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDK 51

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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 6/46 (13%)

Query: 103 KIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
           ++F+G LP +  + EDL R FS +G +  + +        +GFV F
Sbjct: 1   RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKN-----AYGFVQF 41

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFAEEVVADR 155
           ++V  LP+  T ++L   FS +GRI+   +     TG  RG GF+ F + + A+R
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAER 57

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 8/59 (13%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFGFVTF-----AEEVVAD 154
           +++  LP+  T +D+   FSRFGRI++  V V + TG  RG  F+ F     AEE +  
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFG--RILDVYVPKRTGH-RGFGFVTFAEEVVAD 154
           +FV  LP +AT E L  +FS+FG  R     + K TG  +G GFV F ++   +
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN 57

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 16/50 (32%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTG-HRGFGFVTFAEEV 151
           +FVG +       ++R +F+++G + +V  +  RTG  +G+GFV+F ++V
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDV 57

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 6/56 (10%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVT---FAEEVVA 153
           IFV  LP +A    L + FS FG + +V V         +G+GFVT   + E   A
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSA 59

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

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

 Score = 35.2 bits (82), Expect = 0.003
 Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 5/50 (10%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTGHRGFGFVTFAEE 150
           K +F+  LP+E T E L   F++F    +V  VP+    RG  FV F  E
Sbjct: 3   KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR----RGIAFVEFETE 48

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

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

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGHRGFGFVTFAEEVVAD 154
           ++ V  LP+    + LR+ F  FG I DV +   K    R FGFV +  E  A 
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQ 55

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
           ++VG +P   T  DL   F  FG IL+         RGF FV  
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQP---DRGFAFVKL 43

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 3/47 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTF 147
           +FVG L  E T +D++  F+ FGRI D  V K   TG  +G+GFV+F
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           ++VG L +  T +DLR +F +FG I  + V  R   +   FVTF     A++ + R  
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR---QQCAFVTFTTREAAEKAAERLF 58

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV------PKRTGHRGFGFVTFAEEVVADR 155
           ++VG L  + T E L + F RFG +  V +       +R  +R  GFV F     A+R
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 18/50 (36%), Positives = 32/50 (64%), Gaps = 3/50 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEE 150
           I++G LP E T  D+   FS++G I+D+ +   K+TG  +GF F+ + ++
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQ 61

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|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF--AEEVVA 153
           +++G++P   T  +L+  FS FG I +  +  R+    +GFVT+   EE  A
Sbjct: 5   VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYGFVTYRYTEEAFA 56

This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 91

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 3  KDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKED 49
          K  G K  RG GF+ F + DS +   +V  H + G  V V +A PKE+
Sbjct: 35 KQTGKK--RGFGFVYFQNHDSADKAAVVKFHPINGHRVEVKKAVPKEE 80

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

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

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 3/54 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFGFVTFAEEVVAD 154
           ++V  LP+  T ++L + FS++GRI+   + V + TG  RG GF+ F + + A+
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 61

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|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 = 35.0 bits (81), Expect = 0.004
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV--SRRSH 161
           +++G L ++ T EDL+  F  +G I  +        RG  +V       A R     R+ 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSI---DMIPPRGCAYVCMETRQDAHRALQKLRNV 61

Query: 162 EICGQQVAIDSAT 174
           ++ G+++ +  A 
Sbjct: 62  KLAGKKIKVAWAP 74

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

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 5/50 (10%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTGH---RGFGFVTF 147
           K+FVG++P+  + +DLR  F ++G +  ++V   +       +G  FVTF
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 9/82 (10%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGR-ILDVYV----PKRTGHRGFGFVTFAEEVVADRVS 157
           ++F+G +P+E   E++     +    ++DV V      RT +RGF FV +     A    
Sbjct: 4   RLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMAR 63

Query: 158 RR----SHEICGQQVAIDSATP 175
           R+    + ++ G  + +D A P
Sbjct: 64  RKLIPGTFQLWGHTIQVDWACP 85

This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

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

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 3/54 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFGFVTFAEEVVAD 154
           ++V  LP+  T ++L + FS++GRI+   + V + TG  RG GF+ F + + A+
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 58

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	234
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.94
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.94
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.93
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.93
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.92
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.9
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.89
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.88
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.88
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.88
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.86
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.85
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.85
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.82
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.8
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.8
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.8
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.78
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.77
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.75
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.73
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.73
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.72
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.7
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.67
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.64
KOG0122	270	consensus Translation initiation factor 3, subunit	99.63
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.62
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.6
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.57
PLN03213	759	repressor of silencing 3; Provisional	99.56
PLN03121	243	nucleic acid binding protein; Provisional	99.56
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.55
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.55
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.53
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.51
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.51
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.49
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.47
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.46
smart00362	72	RRM_2 RNA recognition motif.	99.44
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.43
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.42
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.42
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.42
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.4
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.38
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.38
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.37
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.36
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.35
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.35
smart00360	71	RRM RNA recognition motif.	99.34
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.33
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.33
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.32
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.32
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.31
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.28
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.26
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.26
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.26
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.24
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.21
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.19
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.16
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.16
smart00361	70	RRM_1 RNA recognition motif.	99.15
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.12
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.09
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.08
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.07
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.06
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.01
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.97
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.97
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.92
KOG4210	285	consensus Nuclear localization sequence binding pr	98.91
KOG0226	290	consensus RNA-binding proteins [General function p	98.91
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.88
smart00361	70	RRM_1 RNA recognition motif.	98.87
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.84
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.82
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.76
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.76
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.75
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.74
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.7
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.7
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.66
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.58
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.58
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.54
KOG0151	877	consensus Predicted splicing regulator, contains R	98.53
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.5
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.5
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.44
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.44
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.44
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.38
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.36
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.28
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.27
smart00360	71	RRM RNA recognition motif.	98.27
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.27
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.25
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.24
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.24
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.23
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.19
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.16
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.15
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.14
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	98.11
PLN03120	260	nucleic acid binding protein; Provisional	98.05
KOG0226	290	consensus RNA-binding proteins [General function p	98.03
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.0
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	97.98
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.9
smart00362	72	RRM_2 RNA recognition motif.	97.9
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	97.86
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.77
PLN03213	759	repressor of silencing 3; Provisional	97.68
PLN03121	243	nucleic acid binding protein; Provisional	97.67
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.66
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.6
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.55
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.55
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.52
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.5
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.45
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.44
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.42
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.29
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.26
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.21
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.08
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	97.05
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.96
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.9
KOG2314	698	consensus Translation initiation factor 3, subunit	96.67
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	96.65
KOG3152	278	consensus TBP-binding protein, activator of basal	96.58
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.57
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.42
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.39
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.35
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	96.17
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.15
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	96.04
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.92
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.89
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	95.77
KOG2135	526	consensus Proteins containing the RNA recognition	94.67
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	94.66
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.66
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	94.63
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.46
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.87
KOG1995	351	consensus Conserved Zn-finger protein [General fun	93.58
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.51
KOG2314	698	consensus Translation initiation factor 3, subunit	92.96
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.29
KOG4210	285	consensus Nuclear localization sequence binding pr	92.09
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	91.55
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.33
KOG4660	549	consensus Protein Mei2, essential for commitment t	91.31
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	91.22
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	90.42
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	90.39
KOG0533	243	consensus RRM motif-containing protein [RNA proces	89.43
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	89.36
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	88.5
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	87.11
KOG2891	445	consensus Surface glycoprotein [General function p	85.85
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	85.57
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	85.38
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	82.88
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	82.26
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	81.01

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=8.2e-30  Score=213.22  Aligned_cols=131  Identities=22%  Similarity=0.353  Sum_probs=112.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|+++||||||+|+++++|++||+  ++..|.+++|+|.++.+...                             
T Consensus       139 i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~-----------------------------  189 (346)
T TIGR01659       139 IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE-----------------------------  189 (346)
T ss_pred             EEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeeccccccc-----------------------------
Confidence            46899999999999999999999999994  68899999999998764321                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~  155 (234)
                                         ....++|||+|||+++|+++|+++|++||.|+.|.|+  +.++ +++||||+|.+.++|++
T Consensus       190 -------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~  250 (346)
T TIGR01659       190 -------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQE  250 (346)
T ss_pred             -------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHH
Confidence                               1235689999999999999999999999999999998  4466 89999999999999999


Q ss_pred             HHh--cCCccCC--eEeEEEeCCCCCCC
Q 026724          156 VSR--RSHEICG--QQVAIDSATPLDDA  179 (234)
Q Consensus       156 A~~--~~~~~~g--~~i~v~~a~~~~~~  179 (234)
                      ||+  +...+.+  ++|+|.++......
T Consensus       251 Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       251 AISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             HHHHhCCCccCCCceeEEEEECCccccc
Confidence            984  6666655  78999999876543

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

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=3.9e-29  Score=193.95  Aligned_cols=144  Identities=26%  Similarity=0.405  Sum_probs=119.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      ||||..|++|||||||.|.+.++|+.||  +++..|.+|.|+-.||..|........                 ..+.  
T Consensus        94 virD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~-----------------ltfd--  154 (321)
T KOG0148|consen   94 VIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKP-----------------LTFD--  154 (321)
T ss_pred             EeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCC-----------------ccHH--
Confidence            6899999999999999999999999999  589999999999999987752111000                 0000  


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                                   ..-.+...+.++|||+|++..+||++|++.|++||.|.+|+|.++   +||+||.|++.|+|..||.
T Consensus       155 -------------eV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~---qGYaFVrF~tkEaAahAIv  218 (321)
T KOG0148|consen  155 -------------EVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD---QGYAFVRFETKEAAAHAIV  218 (321)
T ss_pred             -------------HHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc---cceEEEEecchhhHHHHHH
Confidence                         000112567899999999999999999999999999999999986   7999999999999999984


Q ss_pred             --cCCccCCeEeEEEeCCCCCCC
Q 026724          159 --RSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       159 --~~~~~~g~~i~v~~a~~~~~~  179 (234)
                        |+.+|.|+.|++.|.+.....
T Consensus       219 ~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  219 QMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             HhcCceeCceEEEEeccccCCCC
Confidence              778999999999998865543

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

Probab=99.94  E-value=2e-25  Score=196.05  Aligned_cols=128  Identities=25%  Similarity=0.381  Sum_probs=107.0

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHhc----CceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~~----~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      +..+++++|||||+|++.++|.+|+..    ...|.|+.|.|.|+.++......                          
T Consensus       175 ~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~--------------------------  228 (578)
T TIGR01648       175 AADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED--------------------------  228 (578)
T ss_pred             ccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc--------------------------
Confidence            345678999999999999999999942    34789999999999765432110                          


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhc--CceeEEEeecCCCCcceEEEEEcChHHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF--GRILDVYVPKRTGHRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~  157 (234)
                                       .....++|||+||++++++++|+++|++|  |.|+.|.++     ++||||+|++.++|++|+
T Consensus       229 -----------------~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-----rgfAFVeF~s~e~A~kAi  286 (578)
T TIGR01648       229 -----------------VMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-----RDYAFVHFEDREDAVKAM  286 (578)
T ss_pred             -----------------ccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-----cCeEEEEeCCHHHHHHHH
Confidence                             02345789999999999999999999999  999999875     579999999999999998


Q ss_pred             --hcCCccCCeEeEEEeCCCCCCC
Q 026724          158 --RRSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       158 --~~~~~~~g~~i~v~~a~~~~~~  179 (234)
                        +++.+|+|+.|+|.|++|+...
T Consensus       287 ~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       287 DELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HHhCCCEECCEEEEEEEccCCCcc
Confidence              4778999999999999987543

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.

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

Probab=99.94  E-value=1.3e-25  Score=197.69  Aligned_cols=142  Identities=18%  Similarity=0.393  Sum_probs=114.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|+++||||||+|.+.++|++||.  ++..|+|+.|+|.++..........                        
T Consensus       139 I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~------------------------  194 (612)
T TIGR01645       139 MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPII------------------------  194 (612)
T ss_pred             EeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccccccccccccc------------------------
Confidence            46899999999999999999999999994  7889999999998543221100000                        


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~  155 (234)
                            +       .........++|||+|||+++++++|+++|+.||.|.+|+|+  +.++ ++|||||+|.+.++|.+
T Consensus       195 ------~-------~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~k  261 (612)
T TIGR01645       195 ------D-------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE  261 (612)
T ss_pred             ------c-------cccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHH
Confidence                  0       000012245799999999999999999999999999999998  3456 89999999999999999


Q ss_pred             HH--hcCCccCCeEeEEEeCCCCCCC
Q 026724          156 VS--RRSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       156 A~--~~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      ||  +|+..|+|+.|+|.++.+....
T Consensus       262 AI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       262 AIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             HHHHhCCCeeCCeEEEEEecCCCccc
Confidence            98  4777999999999999875443

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.93  E-value=6.6e-25  Score=186.11  Aligned_cols=80  Identities=21%  Similarity=0.278  Sum_probs=72.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      ..+.+|||+|||+++++++|+++|++||.|.+|+|+  +.++ ++|||||+|.+.++|.+||  +++..|+|+.|+|.|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            344579999999999999999999999999999999  4477 9999999999999999998  4788999999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      .++..
T Consensus       347 ~~~~~  351 (352)
T TIGR01661       347 TNKAY  351 (352)
T ss_pred             cCCCC
Confidence            88764

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

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=2.2e-24  Score=177.80  Aligned_cols=176  Identities=22%  Similarity=0.336  Sum_probs=121.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCcee-CCcEEEEeeccCCCC----------CC----------------
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHEL-GGSTVVVDRATPKED----------DF----------------   51 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i-~gr~i~v~~a~~~~~----------~~----------------   51 (234)
                      |++|+.+|.+||||||+|.+.++|++||.  |+++| .|+.|.|+.+..+..          ..                
T Consensus       115 LMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvd  194 (506)
T KOG0117|consen  115 LMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVD  194 (506)
T ss_pred             EeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeE
Confidence            57899999999999999999999999994  67766 689999987654322          10                


Q ss_pred             -----CCCccCCCCCCCCCCccchhhhhhh----hcCCCCccCCCC------CCCCCCCCCCCCCCEEEEeCCCCCCCHH
Q 026724           52 -----RPVGRMSHGGYGAYNAYISAATRYA----ALGAPTLYDHPG------SFYGRGESSQRIGKKIFVGRLPQEATAE  116 (234)
Q Consensus        52 -----~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~------~~~~~~~~~~~~~~~l~v~nl~~~~~~~  116 (234)
                           .+....-+.++......+..+....    ....-.++....      ......+......+.|||.||+.++||+
T Consensus       195 Vivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE  274 (506)
T KOG0117|consen  195 VIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEE  274 (506)
T ss_pred             EEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHH
Confidence                 0011111111111111122111111    111112222221      1222233345567889999999999999


Q ss_pred             HHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCCCCCCC
Q 026724          117 DLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPLDDAGP  181 (234)
Q Consensus       117 ~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~~~~~~  181 (234)
                      .|+++|++||.|+.|+.++     -||||+|.+.++|.+|+.  |+.+|+|..|+|.+|+|..+..-
T Consensus       275 ~lk~~F~~~G~veRVkk~r-----DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  275 TLKKLFNEFGKVERVKKPR-----DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             HHHHHHHhccceEEeeccc-----ceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhcc
Confidence            9999999999999998864     599999999999999994  78899999999999999765543

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

Probab=99.92  E-value=5.3e-24  Score=186.52  Aligned_cols=139  Identities=24%  Similarity=0.440  Sum_probs=113.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      |++|+.|+++||||||+|.+.++|++|| +++..|.|++|.|..+............                       
T Consensus       121 i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~-----------------------  177 (457)
T TIGR01622       121 CIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAAT-----------------------  177 (457)
T ss_pred             EeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhhhhccc-----------------------
Confidence            5689999999999999999999999999 5788999999999876433221100000                       


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                        ..           ........+|||+|||..+++++|+++|++||.|..|.|+  ..++ ++|||||+|.+.++|.+|
T Consensus       178 --~~-----------~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       178 --HQ-----------PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             --cc-----------CCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence              00           0001236899999999999999999999999999999988  4455 899999999999999999


Q ss_pred             H--hcCCccCCeEeEEEeCCC
Q 026724          157 S--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       157 ~--~~~~~~~g~~i~v~~a~~  175 (234)
                      +  +++..|.|+.|.|.++..
T Consensus       245 ~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       245 LEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHhcCCcEECCEEEEEEEccC
Confidence            8  477899999999999874

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.92  E-value=7.7e-24  Score=179.59  Aligned_cols=129  Identities=26%  Similarity=0.469  Sum_probs=111.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.||+|||||||+|.+.++|++||+  ++..|.|++|.|.++.+...                             
T Consensus        35 i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~-----------------------------   85 (352)
T TIGR01661        35 LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD-----------------------------   85 (352)
T ss_pred             EEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc-----------------------------
Confidence            46899999999999999999999999994  78899999999999865432                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~  155 (234)
                                         ....++|||+|||..+++++|+++|++||.|..+.++  ..++ ++|||||+|++.++|+.
T Consensus        86 -------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~  146 (352)
T TIGR01661        86 -------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADR  146 (352)
T ss_pred             -------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHH
Confidence                               2235689999999999999999999999999999888  3355 89999999999999999


Q ss_pred             HH--hcCCccCC--eEeEEEeCCCCC
Q 026724          156 VS--RRSHEICG--QQVAIDSATPLD  177 (234)
Q Consensus       156 A~--~~~~~~~g--~~i~v~~a~~~~  177 (234)
                      ||  +++..+.+  .+|.|.++....
T Consensus       147 ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       147 AIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHHhCCCccCCCceeEEEEECCCCC
Confidence            98  46666666  678999987654

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=3e-24  Score=176.34  Aligned_cols=134  Identities=26%  Similarity=0.458  Sum_probs=112.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhc---CceeCC--cEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhh
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVD---THELGG--STVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRY   75 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~---~~~i~g--r~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (234)
                      ||||+.|+.|||||||+|.+.++|++|+..   ...|.|  .+|.|++|....+.                         
T Consensus        66 l~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er-------------------------  120 (510)
T KOG0144|consen   66 LIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER-------------------------  120 (510)
T ss_pred             eecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc-------------------------
Confidence            689999999999999999999999999954   446655  67888888754332                         


Q ss_pred             hhcCCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec-CCC-CcceEEEEEcChHHH
Q 026724           76 AALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVA  153 (234)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~-~~~-~~g~afV~f~~~~~a  153 (234)
                                            ....++|||+-|+..+||.+++++|++||.|++|.|++ ..+ +||||||.|.+.+.|
T Consensus       121 ----------------------~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A  178 (510)
T KOG0144|consen  121 ----------------------IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMA  178 (510)
T ss_pred             ----------------------cccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHH
Confidence                                  22467899999999999999999999999999999994 445 999999999999999


Q ss_pred             HHHHhcCC---ccCC--eEeEEEeCCCCCCCCC
Q 026724          154 DRVSRRSH---EICG--QQVAIDSATPLDDAGP  181 (234)
Q Consensus       154 ~~A~~~~~---~~~g--~~i~v~~a~~~~~~~~  181 (234)
                      ..||+.++   .+.|  .+|.|+||.++.++..
T Consensus       179 ~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  179 VAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            99985432   5555  6899999999887653

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.90  E-value=1.8e-23  Score=153.84  Aligned_cols=133  Identities=26%  Similarity=0.540  Sum_probs=114.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      ||+|+.|...+|||||+|.++|||+-|+  +++..|.|++|+|..+......                            
T Consensus        41 iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~~n----------------------------   92 (203)
T KOG0131|consen   41 IPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQKN----------------------------   92 (203)
T ss_pred             cchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEeccccccc----------------------------
Confidence            6899999999999999999999999999  4888999999999988722111                            


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEE-Eee--cCCC-CcceEEEEEcChHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVP--KRTG-HRGFGFVTFAEEVVAD  154 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~-~~~--~~~~-~~g~afV~f~~~~~a~  154 (234)
                                         ...+.+|||+||.++++|..|.+.|+.||.+... .++  .+++ +++|+||.|++.+.+.
T Consensus        93 -------------------l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd  153 (203)
T KOG0131|consen   93 -------------------LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASD  153 (203)
T ss_pred             -------------------ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHH
Confidence                               2345789999999999999999999999998663 444  5667 9999999999999999


Q ss_pred             HHH--hcCCccCCeEeEEEeCCCCCCCC
Q 026724          155 RVS--RRSHEICGQQVAIDSATPLDDAG  180 (234)
Q Consensus       155 ~A~--~~~~~~~g~~i~v~~a~~~~~~~  180 (234)
                      +|+  +++..++.++|.|.++..+...+
T Consensus       154 ~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  154 AAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             HHHHHhccchhcCCceEEEEEEecCCCc
Confidence            998  47889999999999998776544

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

Probab=99.89  E-value=1.1e-22  Score=182.48  Aligned_cols=133  Identities=23%  Similarity=0.376  Sum_probs=112.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|++|+|||||+|.+.++|++||.  +...|.|++|+|.|+.......                           
T Consensus        32 v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~---------------------------   84 (562)
T TIGR01628        32 VCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLR---------------------------   84 (562)
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccccccc---------------------------
Confidence            46899999999999999999999999995  5678999999999875321110                           


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                         .....+|||+|||.++++++|+++|+.||.|.+|.|+ ..++ ++|||||+|.+.++|.+|
T Consensus        85 -------------------~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~A  145 (562)
T TIGR01628        85 -------------------RSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAA  145 (562)
T ss_pred             -------------------ccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHH
Confidence                               1124579999999999999999999999999999998 4556 999999999999999999


Q ss_pred             Hh--cCCccCCeEeEEEeCCCCCCC
Q 026724          157 SR--RSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       157 ~~--~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      +.  ++..+.++.|.|....++.++
T Consensus       146 i~~lng~~~~~~~i~v~~~~~~~~~  170 (562)
T TIGR01628       146 IQKVNGMLLNDKEVYVGRFIKKHER  170 (562)
T ss_pred             HHHhcccEecCceEEEecccccccc
Confidence            84  677999999999877665544

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

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.89  E-value=4.8e-23  Score=159.45  Aligned_cols=129  Identities=25%  Similarity=0.474  Sum_probs=113.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |+||+.||.|-||+||.|.+++||++||.  |+-.|..+.|+|.+|.|...                             
T Consensus        73 LvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~-----------------------------  123 (360)
T KOG0145|consen   73 LVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD-----------------------------  123 (360)
T ss_pred             eeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChh-----------------------------
Confidence            68999999999999999999999999994  78899999999999987544                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~  155 (234)
                                         ......|||.+||..+|..+|+++|++||.|..-+|.  ..++ ++|.+||.|+..++|+.
T Consensus       124 -------------------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~  184 (360)
T KOG0145|consen  124 -------------------SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEE  184 (360)
T ss_pred             -------------------hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHH
Confidence                               3456789999999999999999999999999777766  6678 99999999999999999


Q ss_pred             HH--hcCCccCC--eEeEEEeCCCCC
Q 026724          156 VS--RRSHEICG--QQVAIDSATPLD  177 (234)
Q Consensus       156 A~--~~~~~~~g--~~i~v~~a~~~~  177 (234)
                      ||  ++++.-.|  .+|.|+||....
T Consensus       185 AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  185 AIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             HHHhccCCCCCCCCCCeEEEecCCcc
Confidence            98  47775554  589999997553

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.88  E-value=2e-22  Score=164.45  Aligned_cols=140  Identities=38%  Similarity=0.678  Sum_probs=123.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      +.+|+.|+++|||+||+|++++.+.++|. ..|.|+++.|.++.+.++........                        
T Consensus        38 vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~------------------------   93 (311)
T KOG4205|consen   38 VMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGR------------------------   93 (311)
T ss_pred             EeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCccccccccc------------------------
Confidence            46899999999999999999999999996 48899999999999998876654332                        


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                        .....+|||++||.++++++|+++|++||.|..+.++  ..+. +++|+||+|.+++++.++
T Consensus        94 ------------------~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv  155 (311)
T KOG4205|consen   94 ------------------HLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKV  155 (311)
T ss_pred             ------------------ccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecccccccee
Confidence                              2257899999999999999999999999999888888  4555 999999999999999999


Q ss_pred             H-hcCCccCCeEeEEEeCCCCCCCCCC
Q 026724          157 S-RRSHEICGQQVAIDSATPLDDAGPS  182 (234)
Q Consensus       157 ~-~~~~~~~g~~i~v~~a~~~~~~~~~  182 (234)
                      + +..|.|+++.++|+.|.|++...+.
T Consensus       156 ~~~~f~~~~gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  156 TLQKFHDFNGKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             cccceeeecCceeeEeeccchhhcccc
Confidence            8 5789999999999999999876643

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

Probab=99.88  E-value=1.3e-21  Score=173.61  Aligned_cols=153  Identities=13%  Similarity=0.227  Sum_probs=109.3

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCc
Q 026724            5 QGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTL   83 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (234)
                      ..+.+++|||||+|.+.++|++|| +++..|.|++|.|....................   ....           ....
T Consensus       217 ~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~---~~~~-----------~~~~  282 (509)
T TIGR01642       217 VNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKN---PDDN-----------AKNV  282 (509)
T ss_pred             EEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCccccCCCCCCCC---Cccc-----------cccc
Confidence            345678999999999999999999 478899999999976543321110000000000   0000           0000


Q ss_pred             cCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--h
Q 026724           84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--R  158 (234)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~  158 (234)
                           ..............+|||+|||+.+++++|+++|+.||.|..+.|+  ..++ ++|||||+|.+.++|..||  +
T Consensus       283 -----~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l  357 (509)
T TIGR01642       283 -----EKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL  357 (509)
T ss_pred             -----ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHc
Confidence                 0000001113356799999999999999999999999999999988  4467 9999999999999999998  4


Q ss_pred             cCCccCCeEeEEEeCCCC
Q 026724          159 RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       159 ~~~~~~g~~i~v~~a~~~  176 (234)
                      ++..|.|+.|.|.++...
T Consensus       358 ~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       358 NGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             CCCEECCeEEEEEECccC
Confidence            788999999999998654

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

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

Probab=99.88  E-value=5.8e-22  Score=177.72  Aligned_cols=146  Identities=27%  Similarity=0.481  Sum_probs=113.7

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeC----CcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhh
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELG----GSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRY   75 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~----gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (234)
                      ++| .+++++|||||+|++.++|.+|++  ++..|.    ++.|.|.++..+.........                 ..
T Consensus       211 ~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~-----------------~~  272 (562)
T TIGR01628       211 MKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRR-----------------KF  272 (562)
T ss_pred             EEC-CCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHh-----------------hH
Confidence            345 468999999999999999999994  677888    999999888665432111000                 00


Q ss_pred             hhcCCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHH
Q 026724           76 AALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVA  153 (234)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a  153 (234)
                      ....             ..........+|||+||++.+++++|+++|++||.|++|.|+ +.++ ++|||||+|.+.++|
T Consensus       273 ~~~~-------------~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A  339 (562)
T TIGR01628       273 EELQ-------------QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEA  339 (562)
T ss_pred             Hhhh-------------hhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHH
Confidence            0000             000013356789999999999999999999999999999998 5566 999999999999999


Q ss_pred             HHHHh--cCCccCCeEeEEEeCCCCCC
Q 026724          154 DRVSR--RSHEICGQQVAIDSATPLDD  178 (234)
Q Consensus       154 ~~A~~--~~~~~~g~~i~v~~a~~~~~  178 (234)
                      .+|+.  ++..|.|++|.|.+|..+..
T Consensus       340 ~~A~~~~~g~~~~gk~l~V~~a~~k~~  366 (562)
T TIGR01628       340 NRAVTEMHGRMLGGKPLYVALAQRKEQ  366 (562)
T ss_pred             HHHHHHhcCCeeCCceeEEEeccCcHH
Confidence            99984  67799999999999987653

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

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

Probab=99.88  E-value=4.9e-21  Score=141.50  Aligned_cols=82  Identities=32%  Similarity=0.589  Sum_probs=73.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ...+++|||+|||++++|++|+++|++||.|.+|.|+  +.++ +++||||+|.+.++|++||.  +++.|+|+.|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999998  4566 99999999999999999994  67899999999999


Q ss_pred             CCCCCCC
Q 026724          173 ATPLDDA  179 (234)
Q Consensus       173 a~~~~~~  179 (234)
                      +.++...
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9876554

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=6e-22  Score=167.10  Aligned_cols=156  Identities=26%  Similarity=0.438  Sum_probs=118.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      ++.++.++.+||||||+|+-.||++.|+.  +...|.|+.|.|..|..+...........            .+     .
T Consensus        37 vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~------------~~-----v   99 (678)
T KOG0127|consen   37 VVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGEN------------KA-----V   99 (678)
T ss_pred             EecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccccc------------hh-----h
Confidence            35788899999999999999999999995  46689999999999887655431100000            00     0


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCCCcceEEEEEcChHHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGHRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~~~g~afV~f~~~~~a~~A  156 (234)
                      ..+.....     ........+..+|.|.||||.+.+.+|+.+|+.||.|.+|.|+  .+.+-.|||||+|....+|..|
T Consensus       100 eK~~~q~~-----~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~A  174 (678)
T KOG0127|consen  100 EKPIEQKR-----PTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKA  174 (678)
T ss_pred             hcccccCC-----cchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHH
Confidence            00000000     0001113447899999999999999999999999999999999  3344559999999999999999


Q ss_pred             Hh--cCCccCCeEeEEEeCCCCCC
Q 026724          157 SR--RSHEICGQQVAIDSATPLDD  178 (234)
Q Consensus       157 ~~--~~~~~~g~~i~v~~a~~~~~  178 (234)
                      |.  |++.|.||+|-|.||.++..
T Consensus       175 l~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  175 LEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             HHhccCceecCceeEEeeeccccc
Confidence            94  88999999999999988753

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=8.8e-21  Score=160.12  Aligned_cols=177  Identities=22%  Similarity=0.336  Sum_probs=117.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCc----------------c-CCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVG----------------R-MSHGG   61 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~----------------~-~~~~~   61 (234)
                      ||+.+.++.+ |||||+|.+..+|.+||+  |++.|+||+|.|.||.++........                . ....+
T Consensus       149 IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~  227 (678)
T KOG0127|consen  149 IPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDG  227 (678)
T ss_pred             cccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccc
Confidence            6777776666 999999999999999995  79999999999999988754322110                0 00000


Q ss_pred             CCCCCc---cchhhhhhhhc---------CCCCccCCCCCC--CCCC-----------CCCCCCCCEEEEeCCCCCCCHH
Q 026724           62 YGAYNA---YISAATRYAAL---------GAPTLYDHPGSF--YGRG-----------ESSQRIGKKIFVGRLPQEATAE  116 (234)
Q Consensus        62 ~~~~~~---~~~~~~~~~~~---------~~~~~~~~~~~~--~~~~-----------~~~~~~~~~l~v~nl~~~~~~~  116 (234)
                      -.....   ..+........         ......+...+.  .+..           ........+|||.|||+++|++
T Consensus       228 ~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEE  307 (678)
T KOG0127|consen  228 KDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEE  307 (678)
T ss_pred             cccchhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHH
Confidence            000000   00000000000         000000000000  0000           0112334799999999999999


Q ss_pred             HHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhcC--------CccCCeEeEEEeCCCCCC
Q 026724          117 DLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRRS--------HEICGQQVAIDSATPLDD  178 (234)
Q Consensus       117 ~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~~--------~~~~g~~i~v~~a~~~~~  178 (234)
                      +|.++|++||+|..+.|+  ++|+ ++|.|||.|.+..+|.+||+.-        ..|.||.|.|..|.++.+
T Consensus       308 el~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  308 ELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             HHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHH
Confidence            999999999999998887  8889 9999999999999999998532        478999999999987653

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

Probab=99.85  E-value=4.5e-20  Score=162.23  Aligned_cols=155  Identities=15%  Similarity=0.222  Sum_probs=105.2

Q ss_pred             ccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccc-hhhhhhhhcCCCCccCC
Q 026724           10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYI-SAATRYAALGAPTLYDH   86 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   86 (234)
                      .+|||||+|.+.++|++||  ++++.|.|++|+|.++........... ....+......+. ....++..   +...  
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~-~~~~~~~~~~d~~~~~~~r~~~---~~~~--  385 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREG-QLDDGLTSYKDYSSSRNHRFKK---PGSA--  385 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCC-cCcCCCcccccccCCccccCCC---cccc--
Confidence            4799999999999999999  478899999999998765432111000 0000000000000 00000000   0000  


Q ss_pred             CCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCc--eeEEEeecC-CCCcceEEEEEcChHHHHHHH--hcCC
Q 026724           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVPKR-TGHRGFGFVTFAEEVVADRVS--RRSH  161 (234)
Q Consensus        87 ~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~--v~~~~~~~~-~~~~g~afV~f~~~~~a~~A~--~~~~  161 (234)
                            .......++.+|||+|||+++++++|+++|+.||.  |+.|++... ++.+++|||+|++.++|..||  ++++
T Consensus       386 ------~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~  459 (481)
T TIGR01649       386 ------NKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHH  459 (481)
T ss_pred             ------cccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCC
Confidence                  00011346789999999999999999999999998  788888733 236899999999999999998  4677


Q ss_pred             ccCCeE------eEEEeCCCC
Q 026724          162 EICGQQ------VAIDSATPL  176 (234)
Q Consensus       162 ~~~g~~------i~v~~a~~~  176 (234)
                      .|.++.      |+|.+++++
T Consensus       460 ~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       460 QLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             ccCCCCCCccceEEEEeccCC
Confidence            998885      999999764

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.85  E-value=8.1e-21  Score=167.12  Aligned_cols=122  Identities=26%  Similarity=0.456  Sum_probs=98.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCcee-CCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhh
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHEL-GGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAA   77 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i-~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (234)
                      |++| .||+|||||||+|.+.|+|++||+  ++..| .++.|.|.++.                                
T Consensus        90 l~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~--------------------------------  136 (578)
T TIGR01648        90 LMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV--------------------------------  136 (578)
T ss_pred             EEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc--------------------------------
Confidence            4678 789999999999999999999995  55566 47777665432                                


Q ss_pred             cCCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCc-eeEEEee---cCCC-CcceEEEEEcChHH
Q 026724           78 LGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVP---KRTG-HRGFGFVTFAEEVV  152 (234)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~---~~~~-~~g~afV~f~~~~~  152 (234)
                                            ..++|||+|||+++++++|.++|++++. ++++.+.   .+.+ +++||||+|+++++
T Consensus       137 ----------------------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~ed  194 (578)
T TIGR01648       137 ----------------------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRA  194 (578)
T ss_pred             ----------------------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHH
Confidence                                  2578999999999999999999999864 4444443   2334 89999999999999


Q ss_pred             HHHHHhc----CCccCCeEeEEEeCCCCC
Q 026724          153 ADRVSRR----SHEICGQQVAIDSATPLD  177 (234)
Q Consensus       153 a~~A~~~----~~~~~g~~i~v~~a~~~~  177 (234)
                      |.+|+..    ...+.|+.|.|+|+.++.
T Consensus       195 Aa~AirkL~~gki~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       195 AAMARRKLMPGRIQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             HHHHHHHhhccceEecCceEEEEeecccc
Confidence            9999743    236889999999998764

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.

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

Probab=99.82  E-value=3e-19  Score=157.02  Aligned_cols=131  Identities=14%  Similarity=0.171  Sum_probs=101.4

Q ss_pred             CccceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCcc
Q 026724            9 AHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (234)
                      ++||||||+|++.++|++||.    ++..|.|++|.|.++..+........    .                        
T Consensus        36 ~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~----~------------------------   87 (481)
T TIGR01649        36 PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNS----D------------------------   87 (481)
T ss_pred             CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCC----c------------------------
Confidence            367999999999999999995    46799999999999975532111000    0                        


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCc
Q 026724           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHE  162 (234)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~  162 (234)
                       .       .........+|||.||++.+|+++|+++|+.||.|++|.|+++. .+++|||+|.+.++|.+|+  +++..
T Consensus        88 -~-------~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~-~~~~afVef~~~~~A~~A~~~Lng~~  158 (481)
T TIGR01649        88 -F-------DSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN-NVFQALVEFESVNSAQHAKAALNGAD  158 (481)
T ss_pred             -c-------cCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC-CceEEEEEECCHHHHHHHHHHhcCCc
Confidence             0       00001234579999999999999999999999999999888432 3579999999999999998  47778


Q ss_pred             cCC--eEeEEEeCCCC
Q 026724          163 ICG--QQVAIDSATPL  176 (234)
Q Consensus       163 ~~g--~~i~v~~a~~~  176 (234)
                      |.+  +.|+|.|+++.
T Consensus       159 i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       159 IYNGCCTLKIEYAKPT  174 (481)
T ss_pred             ccCCceEEEEEEecCC
Confidence            865  58999998764

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).

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

Probab=99.81  E-value=5.1e-19  Score=157.07  Aligned_cols=155  Identities=16%  Similarity=0.240  Sum_probs=108.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.||+++|||||+|.+.++|++||+  ++..|.|+.|.|.++.............   .....      .     .
T Consensus       327 ~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~---~~~~~------~-----~  392 (509)
T TIGR01642       327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSN---GMAPV------T-----L  392 (509)
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccc---ccccc------c-----c
Confidence            46888999999999999999999999994  7889999999999986543221111000   00000      0     0


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCC----------CHHHHHHHHhhcCceeEEEeecC-----CC-Ccce
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEA----------TAEDLRRYFSRFGRILDVYVPKR-----TG-HRGF  142 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~----------~~~~l~~~f~~~G~v~~~~~~~~-----~~-~~g~  142 (234)
                      .......      ........++.+|+|.||....          ..++|+++|++||.|+.|.|++.     ++ ..|+
T Consensus       393 ~~~~~~~------~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~  466 (509)
T TIGR01642       393 LAKALSQ------SILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGK  466 (509)
T ss_pred             ccccchh------hhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcce
Confidence            0000000      0000013356789999996421          23679999999999999999832     23 5799


Q ss_pred             EEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          143 GFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       143 afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      +||+|.+.++|++||  +++..|+|+.|.|.|...
T Consensus       467 ~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       467 VFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             EEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            999999999999998  477799999999998753

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

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.80  E-value=3.7e-19  Score=149.97  Aligned_cols=124  Identities=19%  Similarity=0.370  Sum_probs=108.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |.+|. |  |-|||||.|.++++|++||.  |-..|.|++|+|-|+...                               
T Consensus        30 vc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd-------------------------------   75 (369)
T KOG0123|consen   30 VCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD-------------------------------   75 (369)
T ss_pred             EeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC-------------------------------
Confidence            46788 7  99999999999999999995  566999999999988632                               


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCCCcceEEEEEcChHHHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~~~g~afV~f~~~~~a~~A~  157 (234)
                                            ...|||.||+++++..+|.++|+.||.|++|++. +..+++|| ||+|+++++|.+|+
T Consensus        76 ----------------------~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai  132 (369)
T KOG0123|consen   76 ----------------------PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAI  132 (369)
T ss_pred             ----------------------CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHH
Confidence                                  1129999999999999999999999999999999 44559999 99999999999998


Q ss_pred             --hcCCccCCeEeEEEeCCCCCCCCC
Q 026724          158 --RRSHEICGQQVAIDSATPLDDAGP  181 (234)
Q Consensus       158 --~~~~~~~g~~i~v~~a~~~~~~~~  181 (234)
                        +++..+.+++|.|.....++++..
T Consensus       133 ~~~ng~ll~~kki~vg~~~~~~er~~  158 (369)
T KOG0123|consen  133 EKLNGMLLNGKKIYVGLFERKEEREA  158 (369)
T ss_pred             HHhcCcccCCCeeEEeeccchhhhcc
Confidence              477899999999999888777653

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.80  E-value=3e-18  Score=132.96  Aligned_cols=174  Identities=24%  Similarity=0.297  Sum_probs=119.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCC--cEEEEeeccCCCCCCCCC--cc---CCCCCCCCCCccchh
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG--STVVVDRATPKEDDFRPV--GR---MSHGGYGAYNAYISA   71 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~g--r~i~v~~a~~~~~~~~~~--~~---~~~~~~~~~~~~~~~   71 (234)
                      |..|..||.|||.|||.|...++|+.||.  |++.-.|  .+|.|+++..........  ..   .+......+  ....
T Consensus       159 iL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp--~hh~  236 (360)
T KOG0145|consen  159 ILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGP--MHHQ  236 (360)
T ss_pred             hhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCc--ccch
Confidence            45789999999999999999999999994  7776554  679999986543221100  00   000011110  1111


Q ss_pred             hhhh-----------hhcCCCCccCCCCCCCCCC-CCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecC--C
Q 026724           72 ATRY-----------AALGAPTLYDHPGSFYGRG-ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--T  137 (234)
Q Consensus        72 ~~~~-----------~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~--~  137 (234)
                      ..++           .....|...+......+.. +.......+|||-||.++++|..|.++|.+||.|..|+|+++  +
T Consensus       237 ~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~tt  316 (360)
T KOG0145|consen  237 AQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTT  316 (360)
T ss_pred             hhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCc
Confidence            1111           1111222222222222211 122445789999999999999999999999999999999933  3


Q ss_pred             C-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724          138 G-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       138 ~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      . .|||+||++.+.++|..||  +++..+.++.|.|.|...+
T Consensus       317 nkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  317 NKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             ccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            4 9999999999999999998  5888999999999987654

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.80  E-value=4.2e-19  Score=143.66  Aligned_cols=139  Identities=17%  Similarity=0.380  Sum_probs=110.0

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      --|+.|+++||||||+|+-+|.|+-|++  |+..+.||.|+|.+...-...+               ...+....     
T Consensus       146 SWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQ---------------piID~vqe-----  205 (544)
T KOG0124|consen  146 SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQ---------------PIIDMVQE-----  205 (544)
T ss_pred             ccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccc---------------hHHHHHHH-----
Confidence            3489999999999999999999999995  7889999999998543211110               00111000     


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                       ....-++|||..+.++++|+||+..|+.||+|+.|.+.  ...+ +|||+|++|.+..+...|
T Consensus       206 -----------------eAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eA  268 (544)
T KOG0124|consen  206 -----------------EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA  268 (544)
T ss_pred             -----------------HHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHH
Confidence                             02345789999999999999999999999999999998  3333 999999999999999999


Q ss_pred             H--hcCCccCCeEeEEEeCCCCC
Q 026724          157 S--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       157 ~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      |  +|...+.|+-|+|-.+....
T Consensus       269 iasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  269 IASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             hhhcchhhcccceEecccccCCC
Confidence            8  57779999999998875443

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.78  E-value=9.4e-19  Score=152.06  Aligned_cols=130  Identities=29%  Similarity=0.518  Sum_probs=105.9

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDH   86 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (234)
                      .|.|||||+|.++++|++|+.  +++.|+|+.|.|+++..+....-.                                 
T Consensus       558 lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~g---------------------------------  604 (725)
T KOG0110|consen  558 LSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVG---------------------------------  604 (725)
T ss_pred             cccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccc---------------------------------
Confidence            477999999999999999995  588999999999998722211100                                 


Q ss_pred             CCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-c-CCC-CcceEEEEEcChHHHHHHHh--cCC
Q 026724           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-K-RTG-HRGFGFVTFAEEVVADRVSR--RSH  161 (234)
Q Consensus        87 ~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~-~~~-~~g~afV~f~~~~~a~~A~~--~~~  161 (234)
                            ...+.....++|+|.|||+..+..+++++|..||.|.+|+|+ + ... ++|||||+|-+..+|.+|+.  ...
T Consensus       605 ------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~ST  678 (725)
T KOG0110|consen  605 ------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGST  678 (725)
T ss_pred             ------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhccc
Confidence                  000113346799999999999999999999999999999999 3 333 79999999999999999983  466


Q ss_pred             ccCCeEeEEEeCCCCC
Q 026724          162 EICGQQVAIDSATPLD  177 (234)
Q Consensus       162 ~~~g~~i~v~~a~~~~  177 (234)
                      .|.||.|.++||....
T Consensus       679 HlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  679 HLYGRRLVLEWAKSDN  694 (725)
T ss_pred             ceechhhheehhccch
Confidence            8999999999998643

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

Probab=99.77  E-value=1.9e-17  Score=145.24  Aligned_cols=173  Identities=16%  Similarity=0.222  Sum_probs=109.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCcc------CCCCCCCCCCccchhh
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGR------MSHGGYGAYNAYISAA   72 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~------~~~~~~~~~~~~~~~~   72 (234)
                      |++|+.||+++|||||+|.+.++|.+||.  ++..|.|++|.|.++............      ....+...........
T Consensus       218 ~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  297 (457)
T TIGR01622       218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQL  297 (457)
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHH
Confidence            46788999999999999999999999994  788999999999997632211110000      0000000000000000


Q ss_pred             -h---------------------hhhhcCCCCccC--C-----------CC-CCCCCCCCCCCCCCEEEEeCCCCCCC--
Q 026724           73 -T---------------------RYAALGAPTLYD--H-----------PG-SFYGRGESSQRIGKKIFVGRLPQEAT--  114 (234)
Q Consensus        73 -~---------------------~~~~~~~~~~~~--~-----------~~-~~~~~~~~~~~~~~~l~v~nl~~~~~--  114 (234)
                       .                     .+..........  .           .. ..............+|+|.||....+  
T Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~  377 (457)
T TIGR01622       298 MEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEE  377 (457)
T ss_pred             HHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccc
Confidence             0                     000000000000  0           00 00000111235678999999954443  


Q ss_pred             --------HHHHHHHHhhcCceeEEEee-cCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          115 --------AEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       115 --------~~~l~~~f~~~G~v~~~~~~-~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                              .+||++.|++||.|+.|.|. +.  ..|++||+|.++++|.+|+  +++..++|+.|.|.+...
T Consensus       378 ~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~--~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       378 EPNFDNEILDDVKEECSKYGGVVHIYVDTKN--SAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             cchHHHHHHHHHHHHHHhcCCeeEEEEeCCC--CceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence                    36899999999999999887 32  5799999999999999998  578899999999998754

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.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.75  E-value=1.8e-18  Score=146.58  Aligned_cols=142  Identities=25%  Similarity=0.447  Sum_probs=112.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      ||.|+.+++|||.|||+|.+.+....|| +.+..+.|.+|.|+.....+..........                     
T Consensus       211 iI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaeknr~a~~s~a~---------------------  269 (549)
T KOG0147|consen  211 IIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEKNRAANASPAL---------------------  269 (549)
T ss_pred             eeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHHHHHHhccccc---------------------
Confidence            6889999999999999999999999999 589999999999987654332211000000                     


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecC--CC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~--~~-~~g~afV~f~~~~~a~~A  156 (234)
                          .         ......+..+|||+||.+++++++|+.+|+.||.|..|.++.+  +| ++||+||+|.+.++|.+|
T Consensus       270 ----~---------~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a  336 (549)
T KOG0147|consen  270 ----Q---------GKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKA  336 (549)
T ss_pred             ----c---------ccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHH
Confidence                0         0000222334999999999999999999999999999999944  88 999999999999999999


Q ss_pred             H--hcCCccCCeEeEEEeCCCC
Q 026724          157 S--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       157 ~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      +  +|+.+|.|+.|+|.....+
T Consensus       337 ~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  337 LEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             HHHhccceecCceEEEEEeeee
Confidence            7  4788999999999865443

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.73  E-value=1.4e-17  Score=131.04  Aligned_cols=117  Identities=20%  Similarity=0.409  Sum_probs=103.6

Q ss_pred             ccceEEEEEcCHHHHHHHHhc--CceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCC
Q 026724           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (234)
                      =|.||||..++...|+.||.|  +.+|+|..|.|+.+++|                                        
T Consensus        35 vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK----------------------------------------   74 (346)
T KOG0109|consen   35 VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK----------------------------------------   74 (346)
T ss_pred             ecccceEEeecccccHHHHhhcccceecceEEEEEecccc----------------------------------------
Confidence            367999999999999999976  44999999999988765                                        


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCC
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICG  165 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g  165 (234)
                                +..+.+|+|+||.+.++.++|+..|++||.|.+|.|+     ++|+||.|+-.++|..|+  +++.++.|
T Consensus        75 ----------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv-----kdy~fvh~d~~eda~~air~l~~~~~~g  139 (346)
T KOG0109|consen   75 ----------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV-----KDYAFVHFDRAEDAVEAIRGLDNTEFQG  139 (346)
T ss_pred             ----------CCCccccccCCCCccccCHHHhhhhcccCCceeeeee-----cceeEEEEeeccchHHHHhccccccccc
Confidence                      2357899999999999999999999999999999997     469999999999999999  57889999


Q ss_pred             eEeEEEeCCCCCCCCC
Q 026724          166 QQVAIDSATPLDDAGP  181 (234)
Q Consensus       166 ~~i~v~~a~~~~~~~~  181 (234)
                      ++++|..+..+-...+
T Consensus       140 k~m~vq~stsrlrtap  155 (346)
T KOG0109|consen  140 KRMHVQLSTSRLRTAP  155 (346)
T ss_pred             ceeeeeeeccccccCC
Confidence            9999999987665444

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.73  E-value=4.3e-17  Score=120.59  Aligned_cols=77  Identities=23%  Similarity=0.493  Sum_probs=69.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ..+++|||+|||.++.+.+|+++|.+||.|.+|.|....+...||||+|++..+|+.||.  ++..++|..|+|+++..
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            357899999999999999999999999999999987444467899999999999999994  78899999999999874

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.72  E-value=2.3e-16  Score=115.79  Aligned_cols=79  Identities=29%  Similarity=0.569  Sum_probs=71.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..++|||+||+..+++.||+.+|..||+|..|.|...  +.|||||+|++..+|+.|+  +++..|+|..|+|++..-+.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn--PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN--PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec--CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            4789999999999999999999999999999988753  5799999999999999997  78999999999999987665


Q ss_pred             CCC
Q 026724          178 DAG  180 (234)
Q Consensus       178 ~~~  180 (234)
                      ...
T Consensus        87 r~~   89 (195)
T KOG0107|consen   87 RGS   89 (195)
T ss_pred             ccc
Confidence            543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.70  E-value=4e-17  Score=125.16  Aligned_cols=77  Identities=40%  Similarity=0.669  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhcCC-ccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRRSH-EICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~~~-~~~g~~i~v~~a  173 (234)
                      +..-++|||++|+|.+..++|+++|++||+|++..|+  +.++ +|||+||+|.|.++|.+|+++.. .|+||+..|++|
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA   88 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLA   88 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchh
Confidence            4566899999999999999999999999999998888  7788 99999999999999999998765 999999999876


Q ss_pred             C
Q 026724          174 T  174 (234)
Q Consensus       174 ~  174 (234)
                      .
T Consensus        89 ~   89 (247)
T KOG0149|consen   89 S   89 (247)
T ss_pred             h
Confidence            4

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.67  E-value=3.9e-16  Score=124.88  Aligned_cols=79  Identities=32%  Similarity=0.596  Sum_probs=72.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|+|.|||+...+.||+.+|++||.|.+|.|+ .+.|+|||+||+|++.+||++|-  +++..|.||+|+|..|.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            5567899999999999999999999999999999999 77779999999999999999996  46779999999999987


Q ss_pred             CC
Q 026724          175 PL  176 (234)
Q Consensus       175 ~~  176 (234)
                      ++
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            65

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.66  E-value=8.8e-16  Score=128.89  Aligned_cols=80  Identities=25%  Similarity=0.425  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEE
Q 026724           97 SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAID  171 (234)
Q Consensus        97 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~  171 (234)
                      .....++|||+|||+++|+++|+++|+.||.|++|+|+  ..++ ++|||||+|.++++|++||  +++..|.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            35578899999999999999999999999999999998  4566 9999999999999999998  47789999999999


Q ss_pred             eCCCC
Q 026724          172 SATPL  176 (234)
Q Consensus       172 ~a~~~  176 (234)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98764

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.64  E-value=1.7e-15  Score=119.89  Aligned_cols=76  Identities=24%  Similarity=0.305  Sum_probs=69.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~~  176 (234)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.+...++||||+|.+.++|+.|| +++..|.|+.|+|.++..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            579999999999999999999999999999999854446799999999999999998 5888999999999998643

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.63  E-value=3.9e-15  Score=114.79  Aligned_cols=79  Identities=28%  Similarity=0.428  Sum_probs=73.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|-|.||+.+++|++|+++|.+||.|..|.|.  +.|| +||||||+|.+.++|++||  ++++-++.--|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            4467889999999999999999999999999999888  7889 9999999999999999998  588899999999999


Q ss_pred             CCCC
Q 026724          173 ATPL  176 (234)
Q Consensus       173 a~~~  176 (234)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9986

>PF00076 RRM_1: RNA recognition motif

Probab=99.62  E-value=2.2e-15  Score=97.54  Aligned_cols=66  Identities=35%  Similarity=0.758  Sum_probs=60.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhhcCceeEEEeec-CCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeE
Q 026724          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVA  169 (234)
Q Consensus       104 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~-~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~  169 (234)
                      |||+|||+++|+++|+++|++||.|..+.+.. .++ .+++|||+|.+.++|++|+.  ++..+.|+.|+
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            79999999999999999999999999999884 555 89999999999999999984  67899999875

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=2.5e-15  Score=104.77  Aligned_cols=81  Identities=21%  Similarity=0.296  Sum_probs=71.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ...+++|||+||++.++|++|.++|+.+|.|..|.+-  +.+. +.|||||+|.+.++|+.|+  .++..++.+.|+|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            4568999999999999999999999999999988665  5566 8999999999999999998  478899999999999


Q ss_pred             CCCCCC
Q 026724          173 ATPLDD  178 (234)
Q Consensus       173 a~~~~~  178 (234)
                      ...-.+
T Consensus       113 D~GF~e  118 (153)
T KOG0121|consen  113 DAGFVE  118 (153)
T ss_pred             cccchh
Confidence            865443

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.57  E-value=8.1e-14  Score=117.20  Aligned_cols=134  Identities=20%  Similarity=0.314  Sum_probs=102.4

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPT   82 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (234)
                      .+.+|+..|-|||+|++.||+++||++ ...+..|.|.|-.+...+.......                           
T Consensus        42 ~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~~~~~---------------------------   94 (510)
T KOG4211|consen   42 PRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADWVMRP---------------------------   94 (510)
T ss_pred             eccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccccccC---------------------------
Confidence            456899999999999999999999974 5688889999987765543211100                           


Q ss_pred             ccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEee-cCCC-CcceEEEEEcChHHHHHHHh-
Q 026724           83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVP-KRTG-HRGFGFVTFAEEVVADRVSR-  158 (234)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-  158 (234)
                                ..+........|-+.+||+.||++||.++|+..-.|.. |.++ ...+ +.|-|||+|++.+.|++||. 
T Consensus        95 ----------~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen   95 ----------GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             ----------CCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH
Confidence                      00001235678899999999999999999998866655 4444 3334 88999999999999999996 


Q ss_pred             cCCccCCeEeEEEeCC
Q 026724          159 RSHEICGQQVAIDSAT  174 (234)
Q Consensus       159 ~~~~~~g~~i~v~~a~  174 (234)
                      +...|..|-|+|..+.
T Consensus       165 hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  165 HRENIGHRYIEVFRSS  180 (510)
T ss_pred             HHHhhccceEEeehhH
Confidence            5668888889997664

>PLN03213 repressor of silencing 3; Provisional

Probab=99.56  E-value=1.6e-14  Score=121.49  Aligned_cols=78  Identities=21%  Similarity=0.348  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcCh--HHHHHHH--hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE--VVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~--~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      .....+||||||++.+++++|+.+|+.||.|..|.|++.++ ||||||+|.+.  .++.+||  +++..+.|+.|+|..|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG-RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG-RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC-CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            34567999999999999999999999999999999997777 99999999987  6788888  5888999999999999


Q ss_pred             CCC
Q 026724          174 TPL  176 (234)
Q Consensus       174 ~~~  176 (234)
                      +|.
T Consensus        86 KP~   88 (759)
T PLN03213         86 KEH   88 (759)
T ss_pred             cHH
Confidence            863

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.56  E-value=3.1e-14  Score=111.04  Aligned_cols=75  Identities=24%  Similarity=0.264  Sum_probs=68.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      ...+|||+||++.+|+++|+++|+.||.|.+|.|+++...++||||+|.+.++|+.|+ +++..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            4679999999999999999999999999999999966556789999999999999997 69999999999998654

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.55  E-value=2.2e-14  Score=121.16  Aligned_cols=126  Identities=25%  Similarity=0.451  Sum_probs=106.4

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (234)
                      |||| ||+|+++++|++||.  |+..+.+++|.|.....+.....+...                               
T Consensus       115 ~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~-------------------------------  162 (369)
T KOG0123|consen  115 SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE-------------------------------  162 (369)
T ss_pred             ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccc-------------------------------
Confidence            9999 999999999999994  788999999999988776654433211                               


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCcc
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEI  163 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~  163 (234)
                               .......+||.|++.+++++.|.++|..+|.|..+.++ +..+ +++|+||.|.++++|..|+.  ++..+
T Consensus       163 ---------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~  233 (369)
T KOG0123|consen  163 ---------YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIF  233 (369)
T ss_pred             ---------hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcC
Confidence                     02345679999999999999999999999999999999 5555 89999999999999999985  56678


Q ss_pred             CCeEeEEEeCCCC
Q 026724          164 CGQQVAIDSATPL  176 (234)
Q Consensus       164 ~g~~i~v~~a~~~  176 (234)
                      .+..+.|..+..+
T Consensus       234 ~~~~~~V~~aqkk  246 (369)
T KOG0123|consen  234 GDKELYVGRAQKK  246 (369)
T ss_pred             Cccceeecccccc
Confidence            8888888888764

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.55  E-value=3.2e-14  Score=107.21  Aligned_cols=81  Identities=28%  Similarity=0.489  Sum_probs=72.1

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeE
Q 026724           95 ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVA  169 (234)
Q Consensus        95 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~  169 (234)
                      ++.......|-|-||.+.++.++|+.+|++||.|-+|.|+  +-|. ++|||||.|.+..+|+.|+  +++..|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            3335567789999999999999999999999999999999  5567 9999999999999999998  578899999999


Q ss_pred             EEeCCC
Q 026724          170 IDSATP  175 (234)
Q Consensus       170 v~~a~~  175 (234)
                      |.+|+=
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            998863

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.53  E-value=5.9e-14  Score=91.04  Aligned_cols=66  Identities=41%  Similarity=0.737  Sum_probs=56.9

Q ss_pred             EEEeCCCCCCCHHHHHHHHhhcCceeEEEeecC-CC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeE
Q 026724          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-TG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVA  169 (234)
Q Consensus       104 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~-~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~  169 (234)
                      |||+|||+++++++|.++|+.||.|..+.+... .+ .+++|||+|.+.++|..|+.  ++..++|+.|+
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            799999999999999999999999999999832 25 89999999999999999984  45799999875

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 ....

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=4.5e-13  Score=106.21  Aligned_cols=82  Identities=24%  Similarity=0.429  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..+-++|||+-|+++++|..|+..|+.||.|+.|+|+  +.|+ ++|||||+|++..+..+|..  .+..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            3567899999999999999999999999999999999  5688 99999999999999999984  57799999999999


Q ss_pred             CCCCCCC
Q 026724          173 ATPLDDA  179 (234)
Q Consensus       173 a~~~~~~  179 (234)
                      -..+...
T Consensus       178 ERgRTvk  184 (335)
T KOG0113|consen  178 ERGRTVK  184 (335)
T ss_pred             ccccccc
Confidence            8766543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=2.1e-13  Score=106.68  Aligned_cols=83  Identities=27%  Similarity=0.415  Sum_probs=74.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....|+|||-.||.+..+.+|.++|-.||.|.+.+|.  +.|. +|.|+||.|+++.+|+.||  +|+..|.=++|+|..
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            5678999999999999999999999999999988776  7777 9999999999999999998  577889889999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      .+|+....
T Consensus       362 KRPkdanR  369 (371)
T KOG0146|consen  362 KRPKDANR  369 (371)
T ss_pred             cCccccCC
Confidence            99987654

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

Probab=99.49  E-value=1.2e-13  Score=122.47  Aligned_cols=78  Identities=24%  Similarity=0.482  Sum_probs=70.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|+|.+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            3456899999999999999999999999999999998  4567 9999999999999999998  478899999999986


Q ss_pred             CCC
Q 026724          173 ATP  175 (234)
Q Consensus       173 a~~  175 (234)
                      ...
T Consensus       184 p~~  186 (612)
T TIGR01645       184 PSN  186 (612)
T ss_pred             ccc
Confidence            543

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.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.47  E-value=6.3e-14  Score=106.61  Aligned_cols=81  Identities=32%  Similarity=0.550  Sum_probs=72.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhc--CCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRR--SHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~  172 (234)
                      ....++|||++|..+++|.-|...|-+||.|.+|.++  -.++ ++||+||+|+..|+|.+||.|  ..+|.||.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            4567899999999999999999999999999999999  4455 999999999999999999965  5599999999999


Q ss_pred             CCCCCC
Q 026724          173 ATPLDD  178 (234)
Q Consensus       173 a~~~~~  178 (234)
                      |+|..-
T Consensus        87 AkP~ki   92 (298)
T KOG0111|consen   87 AKPEKI   92 (298)
T ss_pred             cCCccc
Confidence            998653

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.46  E-value=2.3e-13  Score=95.88  Aligned_cols=83  Identities=28%  Similarity=0.421  Sum_probs=75.0

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724           96 SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus        96 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      +.+.....|||.++...++|++|.+.|..||+|+++.+-  +.|+ .||||.|+|++.+.|++|+  +|+..|.++.|.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            336678899999999999999999999999999999887  7788 9999999999999999998  4788999999999


Q ss_pred             EeCCCCCC
Q 026724          171 DSATPLDD  178 (234)
Q Consensus       171 ~~a~~~~~  178 (234)
                      .|+.-+.+
T Consensus       147 Dw~Fv~gp  154 (170)
T KOG0130|consen  147 DWCFVKGP  154 (170)
T ss_pred             EEEEecCC
Confidence            99976544

>smart00362 RRM_2 RNA recognition motif

Probab=99.44  E-value=1e-12  Score=84.72  Aligned_cols=69  Identities=39%  Similarity=0.769  Sum_probs=61.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEE
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAID  171 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~  171 (234)
                      +|||.|||..+++++|+++|++||.|..+.+....+ ++++|||+|.+.++|+.|+.  ++..+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            589999999999999999999999999998884435 78999999999999999984  5678899998873

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.43  E-value=1.2e-12  Score=88.17  Aligned_cols=80  Identities=18%  Similarity=0.387  Sum_probs=69.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ......|||.|||+.+|.++..++|.+||.|..|+|-....-+|.|||.|++..+|.+|+  +.+..++++.+.|-+-.+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            345678999999999999999999999999999999733336899999999999999998  467799999999988766


Q ss_pred             CC
Q 026724          176 LD  177 (234)
Q Consensus       176 ~~  177 (234)
                      ..
T Consensus        95 ~~   96 (124)
T KOG0114|consen   95 ED   96 (124)
T ss_pred             HH
Confidence            43

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.42  E-value=2.5e-12  Score=109.62  Aligned_cols=170  Identities=17%  Similarity=0.265  Sum_probs=104.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccC--------CCCCCCCCCccch
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRM--------SHGGYGAYNAYIS   70 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~--------~~~~~~~~~~~~~   70 (234)
                      |++|..||++||||||+|.+.++|.+|++  |+.+|.|+.|+|.....+..........        .....+... ...
T Consensus       310 l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g-~~Q  388 (549)
T KOG0147|consen  310 LTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGG-RNQ  388 (549)
T ss_pred             eccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhcccccccccc-HHH
Confidence            56888999999999999999999999984  7889999999998765543322110000        000000000 001


Q ss_pred             hhhhhhhcCC---CC--------------ccCCCCCC--CCC-----CCCCCCCCCEEEEeCC--CCCCC--------HH
Q 026724           71 AATRYAALGA---PT--------------LYDHPGSF--YGR-----GESSQRIGKKIFVGRL--PQEAT--------AE  116 (234)
Q Consensus        71 ~~~~~~~~~~---~~--------------~~~~~~~~--~~~-----~~~~~~~~~~l~v~nl--~~~~~--------~~  116 (234)
                      ..........   +.              ........  ...     .+.-..++.++.+.|+  |...|        .+
T Consensus       389 l~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~e  468 (549)
T KOG0147|consen  389 LMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIRE  468 (549)
T ss_pred             HHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHH
Confidence            1111100000   00              00000000  000     1111256677778877  22212        35


Q ss_pred             HHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724          117 DLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus       117 ~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      |+.+.+.+||.|..|.|.+.  +-|+.||.|.+.+.|..|+.  ++..|.|+.|.+.|-
T Consensus       469 dV~Eec~k~g~v~hi~vd~n--s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~  525 (549)
T KOG0147|consen  469 DVIEECGKHGKVCHIFVDKN--SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYL  525 (549)
T ss_pred             HHHHHHHhcCCeeEEEEccC--CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEe
Confidence            77788899999999988654  45999999999999999984  666999999999875

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.42  E-value=6.3e-12  Score=96.45  Aligned_cols=160  Identities=16%  Similarity=0.237  Sum_probs=105.2

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCC-
Q 026724            5 QGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAP-   81 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   81 (234)
                      -.|.+.||-|||.|.+.+.|..|+  +++..+.|++++|++|..+...........     ..........+......+ 
T Consensus        46 ~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~-----v~~~~k~~~~~~~~~~~~~  120 (221)
T KOG4206|consen   46 FKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTF-----VEKEKKINGEILARIKQPL  120 (221)
T ss_pred             cCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCcee-----ccccCccccccccccCCcc
Confidence            357899999999999999999999  478899999999999987665432211000     000000000000000000 


Q ss_pred             ---------CccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHH
Q 026724           82 ---------TLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVV  152 (234)
Q Consensus        82 ---------~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~  152 (234)
                               ...+.+...  . .....+...||+.|||..++.+.|..+|.+|.-..+|+++..  .++.|||+|.+...
T Consensus       121 ~~ng~~~~~~~~~~p~p~--~-~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~--~~~iAfve~~~d~~  195 (221)
T KOG4206|consen  121 DTNGHFYNMNRMNLPPPF--L-AQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP--RSGIAFVEFLSDRQ  195 (221)
T ss_pred             cccccccccccccCCCCc--c-ccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC--CCceeEEecchhhh
Confidence                     000000000  1 233667889999999999999999999999999999999843  36899999999887


Q ss_pred             HHHHHh--cCC-ccCCeEeEEEeCC
Q 026724          153 ADRVSR--RSH-EICGQQVAIDSAT  174 (234)
Q Consensus       153 a~~A~~--~~~-~~~g~~i~v~~a~  174 (234)
                      |..|..  .+. .-....+.|.+++
T Consensus       196 a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  196 ASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hHHHhhhhccceeccCceEEecccC
Confidence            777753  222 3336777777764

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.42  E-value=2.6e-12  Score=109.18  Aligned_cols=79  Identities=28%  Similarity=0.482  Sum_probs=67.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cC--CCCcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KR--TGHRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~--~~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~~~  176 (234)
                      ...|||.|||.++++++|+++|.+||.|+...|. +.  .....||||+|.+.++++.||+ +...|++++|.|+..++.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecccc
Confidence            3459999999999999999999999999998877 33  2244999999999999999996 567999999999987765


Q ss_pred             CCC
Q 026724          177 DDA  179 (234)
Q Consensus       177 ~~~  179 (234)
                      ...
T Consensus       368 ~~g  370 (419)
T KOG0116|consen  368 FRG  370 (419)
T ss_pred             ccc
Confidence            544

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.40  E-value=6.5e-13  Score=98.32  Aligned_cols=78  Identities=24%  Similarity=0.502  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      .....+|||+||+..++++.|.++|-+.|+|.++.++  +.+. .+|||||+|.++++|+-|+  +++..|.|++|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            3457899999999999999999999999999999999  5566 8999999999999999996  588899999999999


Q ss_pred             CCC
Q 026724          173 ATP  175 (234)
Q Consensus       173 a~~  175 (234)
                      +..
T Consensus        86 as~   88 (203)
T KOG0131|consen   86 ASA   88 (203)
T ss_pred             ccc
Confidence            873

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.38  E-value=1.2e-12  Score=102.58  Aligned_cols=77  Identities=30%  Similarity=0.483  Sum_probs=70.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ...+||+.|...++-++|++.|.+||+|.+++|++  .|+ +|||+||.|-+.++|+.||  +++.-|.+|.|+..||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            46799999999999999999999999999999994  355 9999999999999999999  578899999999999977


Q ss_pred             CC
Q 026724          176 LD  177 (234)
Q Consensus       176 ~~  177 (234)
                      |.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            65

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.38  E-value=6.4e-14  Score=103.57  Aligned_cols=76  Identities=28%  Similarity=0.534  Sum_probs=68.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      -..+.-|||+|||+.+||.||.-+|++||+|++|.++  +.|| ++||||+.|++..+..-|+  +|+..|.||.|+|..
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            3457789999999999999999999999999999999  6788 9999999999999888888  467799999999985


Q ss_pred             C
Q 026724          173 A  173 (234)
Q Consensus       173 a  173 (234)
                      .
T Consensus       112 v  112 (219)
T KOG0126|consen  112 V  112 (219)
T ss_pred             c
Confidence            4

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=7e-11  Score=87.89  Aligned_cols=124  Identities=22%  Similarity=0.320  Sum_probs=90.4

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (234)
                      .-.||||+|+++.||+.||.  ++..++|..|+|+++..-.........-+..+.+..                      
T Consensus        44 ~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGg----------------------  101 (241)
T KOG0105|consen   44 PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGG----------------------  101 (241)
T ss_pred             CCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCcccccccccCCCCCCCC----------------------
Confidence            34699999999999999994  788999999999998754322111111110100000                      


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhc
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR  159 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~  159 (234)
                      .......++......+|.|.+||++.+|+||+++..+-|.|....+.++    +.+.|+|...|+.+-||.+
T Consensus       102 g~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD----g~GvV~~~r~eDMkYAvr~  169 (241)
T KOG0105|consen  102 GGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD----GVGVVEYLRKEDMKYAVRK  169 (241)
T ss_pred             CCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc----cceeeeeeehhhHHHHHHh
Confidence            0011122333556788999999999999999999999999988888765    7999999999999999843

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.36  E-value=1e-12  Score=103.95  Aligned_cols=70  Identities=29%  Similarity=0.657  Sum_probs=64.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcC--CccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRS--HEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~--~~~~g~~i~v~~a~~~  176 (234)
                      .+|||+|||.++++.+|+.+|++||+|++|.|++     .|+||..++...|+.||.|.  ..|+|..|.|+.++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK-----NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK-----NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec-----ccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            4799999999999999999999999999999984     69999999999999999754  4999999999998877

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=8.5e-12  Score=103.96  Aligned_cols=75  Identities=27%  Similarity=0.565  Sum_probs=66.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCcc-CCeEeEEEe
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEI-CGQQVAIDS  172 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~-~g~~i~v~~  172 (234)
                      ...+.|||+.||.++.|++|.-+|++.|+|-+++|+  +.++ +||||||+|.+.++|+.||.  |.++| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            568899999999999999999999999999999999  5788 99999999999999999984  56655 577777765


Q ss_pred             C
Q 026724          173 A  173 (234)
Q Consensus       173 a  173 (234)
                      +
T Consensus       161 S  161 (506)
T KOG0117|consen  161 S  161 (506)
T ss_pred             e
Confidence            5

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.35  E-value=1.3e-11  Score=102.76  Aligned_cols=79  Identities=16%  Similarity=0.352  Sum_probs=69.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHH-hhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYF-SRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f-~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...+.+||.|||+++.|++|+++| ++.|+|+.|.+. ...+ ++|||.|+|+++|.+++|++  +.++++||+|.|+-.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            345569999999999999999999 568999999988 6666 99999999999999999984  678999999999876


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      ...+
T Consensus       122 ~d~q  125 (608)
T KOG4212|consen  122 HDEQ  125 (608)
T ss_pred             Cchh
Confidence            5544

>smart00360 RRM RNA recognition motif

Probab=99.34  E-value=6e-12  Score=80.71  Aligned_cols=66  Identities=39%  Similarity=0.719  Sum_probs=57.7

Q ss_pred             EeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEE
Q 026724          106 VGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAID  171 (234)
Q Consensus       106 v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~  171 (234)
                      |+|||..+++++|+++|++||.|..+.+.  +.++ ++++|||+|.+.++|..|+.  +...+.++.|.|+
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            57999999999999999999999999888  3345 89999999999999999984  5568889988873

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

Probab=99.33  E-value=7.6e-12  Score=101.68  Aligned_cols=75  Identities=37%  Similarity=0.721  Sum_probs=68.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ..+|||+|||+.+++++|.++|.+||.|..+.+.  +.++ ++|||||+|.+.++|..|+.  ++..|.|+.|.|.++.+
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            5999999999999999999999999999999888  3467 99999999999999999984  56799999999999654

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.33  E-value=3.9e-12  Score=105.52  Aligned_cols=82  Identities=27%  Similarity=0.522  Sum_probs=70.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh---cCCccCC--eEeE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR---RSHEICG--QQVA  169 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~---~~~~~~g--~~i~  169 (234)
                      +...-+|||+-+|..++|.||+++|++||.|.+|.|+  +.++ ++|||||.|.+.++|.+|+.   |...|-|  .+|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            4567799999999999999999999999999999999  5577 99999999999999999873   4556666  5889


Q ss_pred             EEeCCCCCCC
Q 026724          170 IDSATPLDDA  179 (234)
Q Consensus       170 v~~a~~~~~~  179 (234)
                      |++|....++
T Consensus       111 vk~Ad~E~er  120 (510)
T KOG0144|consen  111 VKYADGERER  120 (510)
T ss_pred             ecccchhhhc
Confidence            9999876655

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.32  E-value=1.4e-11  Score=107.90  Aligned_cols=160  Identities=19%  Similarity=0.244  Sum_probs=98.2

Q ss_pred             EEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCCC---
Q 026724           14 GFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPG---   88 (234)
Q Consensus        14 aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---   88 (234)
                      |.|+|.++.+|.+|+.  +...+...++.+.|+........+....-. .............+......+...+...   
T Consensus       424 aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~-~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~  502 (725)
T KOG0110|consen  424 AIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLS-AESRSKMEENPSERVSAEDGQVEEDKDPTEE  502 (725)
T ss_pred             eeeeecCccchHHHHHHhchhhhccCccccccChhhhccCCccccccc-cccccccccCcceecccccccccccCCcccc
Confidence            8999999999999995  445666777777776322111000000000 0000000001111111111111111110   


Q ss_pred             CCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC--C--CcceEEEEEcChHHHHHHHh--cC
Q 026724           89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT--G--HRGFGFVTFAEEVVADRVSR--RS  160 (234)
Q Consensus        89 ~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~--~--~~g~afV~f~~~~~a~~A~~--~~  160 (234)
                      +............++|||.||++++|.++|..+|...|.|.++.|.  ++.  .  +.|||||+|.+.++|+.|+.  ++
T Consensus       503 ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqg  582 (725)
T KOG0110|consen  503 SSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQG  582 (725)
T ss_pred             ccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcC
Confidence            0000011112223349999999999999999999999999999888  221  2  66999999999999999984  57


Q ss_pred             CccCCeEeEEEeCC
Q 026724          161 HEICGQQVAIDSAT  174 (234)
Q Consensus       161 ~~~~g~~i~v~~a~  174 (234)
                      +.|+|+.|.|+++.
T Consensus       583 tvldGH~l~lk~S~  596 (725)
T KOG0110|consen  583 TVLDGHKLELKISE  596 (725)
T ss_pred             ceecCceEEEEecc
Confidence            89999999999998

>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=99.32  E-value=2.2e-11  Score=78.74  Aligned_cols=70  Identities=34%  Similarity=0.700  Sum_probs=60.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecC-C-CCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-T-GHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~-~-~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      +|+|+|||..+++++|+++|+.+|.|..+.+... . ..+++|||+|.+.++|..|+.  +...++++.|.|.+
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            4899999999999999999999999999988833 2 268999999999999999985  45568999998864

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).

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.31  E-value=5.6e-12  Score=107.76  Aligned_cols=79  Identities=32%  Similarity=0.595  Sum_probs=72.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      +.|||+|+|+++++++|.++|+..|.|.+++++  +++| ++||+|++|.+.++|..|+  +++.++.|++|+|.|+...
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            899999999999999999999999999999998  7788 9999999999999999998  4778999999999999766


Q ss_pred             CCCC
Q 026724          177 DDAG  180 (234)
Q Consensus       177 ~~~~  180 (234)
                      ..+.
T Consensus        99 ~~~~  102 (435)
T KOG0108|consen   99 KNAE  102 (435)
T ss_pred             chhH
Confidence            5443

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=7.1e-12  Score=96.96  Aligned_cols=132  Identities=23%  Similarity=0.397  Sum_probs=97.2

Q ss_pred             ccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCC
Q 026724           10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (234)
                      -.||+||+|.+.-+|+.||  +++..|.+..+.|.++..........       .++...              .     
T Consensus        34 k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~-------~~g~r~--------------~-----   87 (216)
T KOG0106|consen   34 KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRP-------RGGDRR--------------S-----   87 (216)
T ss_pred             ecccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCC-------CCCCcc--------------c-----
Confidence            3579999999999999999  57888888888888887543322000       000000              0     


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCC
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICG  165 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g  165 (234)
                        ....-.....+.+.|.|.+|+..+.+.+|.+.|.++|++....+     ..+++||+|++.++|..|+.  .+..+.+
T Consensus        88 --~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-----~~~~~~v~Fs~~~da~ra~~~l~~~~~~~  160 (216)
T KOG0106|consen   88 --DSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-----RRNFAFVEFSEQEDAKRALEKLDGKKLNG  160 (216)
T ss_pred             --hhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-----hccccceeehhhhhhhhcchhccchhhcC
Confidence              00001112556789999999999999999999999999965544     36899999999999999984  6779999


Q ss_pred             eEeEEEeCC
Q 026724          166 QQVAIDSAT  174 (234)
Q Consensus       166 ~~i~v~~a~  174 (234)
                      +.|.+.+..
T Consensus       161 ~~l~~~~~~  169 (216)
T KOG0106|consen  161 RRISVEKNS  169 (216)
T ss_pred             ceeeecccC
Confidence            999995443

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.26  E-value=2.6e-11  Score=98.24  Aligned_cols=80  Identities=25%  Similarity=0.461  Sum_probs=70.4

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh---cCCccCCeEeEEE
Q 026724           95 ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR---RSHEICGQQVAID  171 (234)
Q Consensus        95 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~---~~~~~~g~~i~v~  171 (234)
                      ++.+....+|||++|...++|.+|+++|.+||+|+++++...   +++|||+|.+.++|+.|.+   +...|+|++|.|.
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~---~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR---KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc---cccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            344667889999999999999999999999999999999843   5799999999999999974   4558999999999


Q ss_pred             eCCCCC
Q 026724          172 SATPLD  177 (234)
Q Consensus       172 ~a~~~~  177 (234)
                      |..++.
T Consensus       299 Wg~~~~  304 (377)
T KOG0153|consen  299 WGRPKQ  304 (377)
T ss_pred             eCCCcc
Confidence            999843

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.26  E-value=9e-11  Score=89.80  Aligned_cols=153  Identities=20%  Similarity=0.261  Sum_probs=89.1

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeC---CcEEEEeeccCCCCCCCCCccCCCCC--CCCCCccchhhhhhh-
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELG---GSTVVVDRATPKEDDFRPVGRMSHGG--YGAYNAYISAATRYA-   76 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~---gr~i~v~~a~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~-   76 (234)
                      +....++=+|||+|.+..+|.+|+.  |+..++   +..|+|++|++..+..+.......+.  ......+...+.... 
T Consensus        71 k~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~  150 (284)
T KOG1457|consen   71 KGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSAD  150 (284)
T ss_pred             CCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccch
Confidence            3334456799999999999999993  777775   67899999876544333222111110  000000000000000 


Q ss_pred             -----------hcCC----CCccCCC--------------CC------CCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHH
Q 026724           77 -----------ALGA----PTLYDHP--------------GS------FYGRGESSQRIGKKIFVGRLPQEATAEDLRRY  121 (234)
Q Consensus        77 -----------~~~~----~~~~~~~--------------~~------~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~  121 (234)
                                 ....    +.+....              ..      .............+|||.||..+++|++|+.+
T Consensus       151 ~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~  230 (284)
T KOG1457|consen  151 DQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQL  230 (284)
T ss_pred             hhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHH
Confidence                       0000    0000000              00      00001112334568999999999999999999


Q ss_pred             HhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724          122 FSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus       122 f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      |+.|--...++|.... ....|||+|++.+.|..|+.
T Consensus       231 ~~~~~gf~~l~~~~~~-g~~vaf~~~~~~~~at~am~  266 (284)
T KOG1457|consen  231 LSRYPGFHILKIRARG-GMPVAFADFEEIEQATDAMN  266 (284)
T ss_pred             HHhCCCceEEEEecCC-CcceEeecHHHHHHHHHHHH
Confidence            9999887777776222 34689999999999999973

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.26  E-value=6.5e-12  Score=103.01  Aligned_cols=81  Identities=43%  Similarity=0.672  Sum_probs=73.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATP  175 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~~  175 (234)
                      ..++|||++|+|+++++.|+++|.+||+|.+|.++  +.++ +++|+||+|++.+....+|. ..|.|+|+.|.++.|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            57899999999999999999999999999999999  5567 99999999999999888885 57899999999999998


Q ss_pred             CCCCC
Q 026724          176 LDDAG  180 (234)
Q Consensus       176 ~~~~~  180 (234)
                      +....
T Consensus        85 r~~~~   89 (311)
T KOG4205|consen   85 REDQT   89 (311)
T ss_pred             ccccc
Confidence            87544

>PF13893 RRM_5: RNA recognition motif

Probab=99.24  E-value=6.1e-11  Score=73.28  Aligned_cols=54  Identities=30%  Similarity=0.562  Sum_probs=47.5

Q ss_pred             HHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724          118 LRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus       118 l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      |.++|++||.|..+.+.+..  +++|||+|.+.++|..|+.  ++..+.|++|+|.||
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            68899999999999998542  5999999999999999984  788999999999986

(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 ....

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=2e-11  Score=95.64  Aligned_cols=81  Identities=27%  Similarity=0.486  Sum_probs=69.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec-CCC-CcceEEEEEcChHHHHHHHhcCC---ccCC--eEeEEEe
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADRVSRRSH---EICG--QQVAIDS  172 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~-~~~-~~g~afV~f~~~~~a~~A~~~~~---~~~g--~~i~v~~  172 (234)
                      ..++|||+-|...-.|+|++.+|..||.|.+|.+.+ ..+ +|||+||.|.+..+|..||...|   .+-|  ..|.|++
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            578999999999999999999999999999999983 344 99999999999999999985433   4544  5799999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +....++.
T Consensus        98 ADTdkER~  105 (371)
T KOG0146|consen   98 ADTDKERT  105 (371)
T ss_pred             ccchHHHH
Confidence            98776654

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.19  E-value=4.6e-10  Score=93.62  Aligned_cols=170  Identities=20%  Similarity=0.325  Sum_probs=103.0

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCcc-C-----------------CCCCC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGR-M-----------------SHGGY   62 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~-~-----------------~~~~~   62 (234)
                      .|. +|++||+|.|+|+++|.+++|++  +.+.+.||+|.|+.....+..+..... .                 .....
T Consensus        79 ~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g  157 (608)
T KOG4212|consen   79 FDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGG  157 (608)
T ss_pred             ccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccC
Confidence            343 59999999999999999999995  688999999999865443222211000 0                 00000


Q ss_pred             --CCCC--ccch----hhhh----------hhhcCCCCccCCCCCCC-CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHh
Q 026724           63 --GAYN--AYIS----AATR----------YAALGAPTLYDHPGSFY-GRGESSQRIGKKIFVGRLPQEATAEDLRRYFS  123 (234)
Q Consensus        63 --~~~~--~~~~----~~~~----------~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~  123 (234)
                        +...  ....    ...+          ....+...+........ ....-..+...++||.||.+.+....|++.|.
T Consensus       158 ~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfg  237 (608)
T KOG4212|consen  158 GGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFG  237 (608)
T ss_pred             CCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhc
Confidence              0000  0000    0000          00000000000000000 00111244567899999999999999999999


Q ss_pred             hcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724          124 RFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus       124 ~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      -.|.|..|.+- ...+ ++||+.++|..+-+|..||  ++..-+..++..+...
T Consensus       238 mAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  238 MAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLD  291 (608)
T ss_pred             cceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCccccceeecc
Confidence            99999988776 4445 9999999999988888887  3444555666666553

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.16  E-value=2.5e-09  Score=90.50  Aligned_cols=71  Identities=23%  Similarity=0.255  Sum_probs=55.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEe
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDS  172 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~  172 (234)
                      ...++..+||+..++.+|..+|+..-.+ .|.|. ..++ ..|-|+|+|.+.++|..|+. +...+..+-|++..
T Consensus       281 g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~edav~Amskd~anm~hrYVElFl  354 (510)
T KOG4211|consen  281 GHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDAVGAMGKDGANMGHRYVELFL  354 (510)
T ss_pred             CceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhhHhhhccCCcccCcceeeecc
Confidence            3778899999999999999999886555 44444 4455 88999999999999999995 44466666666544

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.16  E-value=5.4e-11  Score=96.62  Aligned_cols=79  Identities=25%  Similarity=0.434  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      .++.+.|||.-|.+-++.++|+-+|+.||.|.+|.|+  +.|+ +..||||+|++.+++++|.  +....|+.+.|+|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            5567899999999999999999999999999999999  6677 9999999999999999997  455689999999999


Q ss_pred             CCCC
Q 026724          173 ATPL  176 (234)
Q Consensus       173 a~~~  176 (234)
                      +++-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8643

>smart00361 RRM_1 RNA recognition motif

Probab=99.15  E-value=1.9e-10  Score=74.42  Aligned_cols=56  Identities=27%  Similarity=0.367  Sum_probs=47.9

Q ss_pred             HHHHHHHHh----hcCceeEEE-ee--cCC--C-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724          115 AEDLRRYFS----RFGRILDVY-VP--KRT--G-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus       115 ~~~l~~~f~----~~G~v~~~~-~~--~~~--~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      +++|+++|+    +||.|.+|. |+  +.+  + ++||+||+|.+.++|.+|+  +++..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999999985 43  444  6 9999999999999999998  4788999999986

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.12  E-value=1.9e-09  Score=89.27  Aligned_cols=149  Identities=12%  Similarity=0.119  Sum_probs=104.6

Q ss_pred             ceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCCCC
Q 026724           12 GIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGS   89 (234)
Q Consensus        12 G~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (234)
                      =-|.|++.+...|+-|++  +++.|.|++|+|.+++...-.  .......+...+.....+.-.|+.........+.   
T Consensus       336 d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq--lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni---  410 (492)
T KOG1190|consen  336 DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ--LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNI---  410 (492)
T ss_pred             cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc--CCCCCCccccccccCCCCchhhccCccccccccc---
Confidence            369999999999999994  899999999999887544322  1111112222233333444555554444444333   


Q ss_pred             CCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEeecCCCCcceEEEEEcChHHHHHHHhcC--CccCCe
Q 026724           90 FYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPKRTGHRGFGFVTFAEEVVADRVSRRS--HEICGQ  166 (234)
Q Consensus        90 ~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~~~~~~g~afV~f~~~~~a~~A~~~~--~~~~g~  166 (234)
                              .+++.+|++.|+|.+++|++|+.+|..-|-... ..+...  .+.++.+.+++.|+|..|+...  |.+...
T Consensus       411 --------~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~k--d~kmal~q~~sveeA~~ali~~hnh~lgen  480 (492)
T KOG1190|consen  411 --------FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQK--DRKMALPQLESVEEAIQALIDLHNHYLGEN  480 (492)
T ss_pred             --------CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCC--CcceeecccCChhHhhhhccccccccCCCC
Confidence                    456789999999999999999999988775543 344321  3679999999999999998544  566544


Q ss_pred             -EeEEEeCCC
Q 026724          167 -QVAIDSATP  175 (234)
Q Consensus       167 -~i~v~~a~~  175 (234)
                       .++|+|++.
T Consensus       481 ~hlRvSFSks  490 (492)
T KOG1190|consen  481 HHLRVSFSKS  490 (492)
T ss_pred             ceEEEEeecc
Confidence             889999874

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=9.3e-11  Score=95.68  Aligned_cols=75  Identities=25%  Similarity=0.524  Sum_probs=67.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      -.++|||+.+.+++.|+.|+..|..||+|++|.+.  ..|+ +||||||+|+-+|.|+-|++  |+..+.||.|+|....
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            46899999999999999999999999999999888  5577 99999999999999999984  7789999999997443

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

Probab=99.08  E-value=2.1e-10  Score=84.84  Aligned_cols=49  Identities=24%  Similarity=0.472  Sum_probs=44.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+++||||||+|++.++|++||+  +++.|+|++|+|+++.++..
T Consensus        66 i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         66 VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            46899999999999999999999999995  68899999999999976654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.07  E-value=7.8e-10  Score=85.04  Aligned_cols=79  Identities=28%  Similarity=0.473  Sum_probs=69.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHH----HHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724          100 IGKKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~----~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      +..+|||.||+..+..++|+.    +|++||.|.+|...+..+.+|-|||.|.+.+.|..|+  +++..+.|+.++|.||
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            344999999999999999888    9999999999988755558999999999999999998  4777999999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      +.+..
T Consensus        88 ~s~sd   92 (221)
T KOG4206|consen   88 KSDSD   92 (221)
T ss_pred             cCccc
Confidence            87643

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.06  E-value=4.9e-10  Score=99.22  Aligned_cols=80  Identities=20%  Similarity=0.412  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ...+++|||+.|+.+++|.||..+|+.||+|.+|.++.   +++||||.+....+|.+|+.  +.+.+..+.|+|.|+..
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~---~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP---PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc---CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            45678999999999999999999999999999998875   47999999999999999985  56689999999999987


Q ss_pred             CCCCC
Q 026724          176 LDDAG  180 (234)
Q Consensus       176 ~~~~~  180 (234)
                      +..+.
T Consensus       495 ~G~ks  499 (894)
T KOG0132|consen  495 KGPKS  499 (894)
T ss_pred             CCcch
Confidence            76554

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.01  E-value=1.1e-09  Score=94.54  Aligned_cols=150  Identities=19%  Similarity=0.288  Sum_probs=100.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      +++|..||-|+||||.+|.++...+.|+.  |+..+.+++|.|..|..............+.                  
T Consensus       321 lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~------------------  382 (500)
T KOG0120|consen  321 LVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQS------------------  382 (500)
T ss_pred             eecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCcccc------------------
Confidence            46899999999999999999999999994  7889999999999987654433322210000                  


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCC--CCCC-CH-------HHHHHHHhhcCceeEEEeecC--C---C-Ccce
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRL--PQEA-TA-------EDLRRYFSRFGRILDVYVPKR--T---G-HRGF  142 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl--~~~~-~~-------~~l~~~f~~~G~v~~~~~~~~--~---~-~~g~  142 (234)
                      +.+.....      .......++..|.+.|+  |.++ ++       ++++..+.+||.|..|.+++.  .   . ..|.
T Consensus       383 ~~~~i~~~------~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~Gk  456 (500)
T KOG0120|consen  383 QVPGIPLL------MTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGK  456 (500)
T ss_pred             ccccchhh------hcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCccc
Confidence            00000000      00011233444544444  1111 22       345667789999999999833  1   1 5678


Q ss_pred             EEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          143 GFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       143 afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      .||+|.+.+++++|+  +.+..+.+|.|...|-.
T Consensus       457 VFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  457 VFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             EEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            899999999999998  46779999999988764

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.97  E-value=5.1e-09  Score=90.16  Aligned_cols=80  Identities=26%  Similarity=0.572  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee---cCCCCcceEEEEEcChHHHHHHHhcCC--ccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~---~~~~~~g~afV~f~~~~~a~~A~~~~~--~~~g~~i~v~~  172 (234)
                      ....++|||.+|+..+...+|+.+|++||.|+-..|+   +..+.+.|+||++.+.++|.+||.+.|  +|.|+.|.|+.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            4456889999999999999999999999999988888   444488999999999999999997765  99999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      ++...
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            87643

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.97  E-value=1.6e-09  Score=93.53  Aligned_cols=146  Identities=19%  Similarity=0.287  Sum_probs=106.2

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            7 SKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      ....+.||||+|.+.++|..|+. +...+.|+++.+.................+                       ...
T Consensus       219 ~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~-----------------------~~~  275 (500)
T KOG0120|consen  219 LNLEKNFAFIEFRSISEATEAMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQ-----------------------LGK  275 (500)
T ss_pred             ecccccceeEEecCCCchhhhhcccchhhCCCCceecccccccCCccchhhhcc-----------------------ccc
Confidence            45678899999999999999994 677889999888655433322111000000                       000


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcC
Q 026724           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRS  160 (234)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~  160 (234)
                      .  ..............++||++||..+++++++++...||.+....++  ..++ +++|||.+|-+......|+  +++
T Consensus       276 ~--~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnG  353 (500)
T KOG0120|consen  276 V--GLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNG  353 (500)
T ss_pred             c--CCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccch
Confidence            0  0000011114456789999999999999999999999999988887  4556 9999999999999888887  578


Q ss_pred             CccCCeEeEEEeCCCCC
Q 026724          161 HEICGQQVAIDSATPLD  177 (234)
Q Consensus       161 ~~~~g~~i~v~~a~~~~  177 (234)
                      ..+.+..|.|..|.+..
T Consensus       354 m~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  354 MQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             hhhcCceeEeehhhccc
Confidence            89999999999886544

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.92  E-value=5.8e-10  Score=86.10  Aligned_cols=46  Identities=22%  Similarity=0.385  Sum_probs=42.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~~   46 (234)
                      ||.|+.|++|||||||+|.|.|.|.+|+++ ...|+||+..|++|.-
T Consensus        44 vitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   44 VITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            578999999999999999999999999987 5699999999998864

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.91  E-value=5.2e-09  Score=85.64  Aligned_cols=137  Identities=23%  Similarity=0.326  Sum_probs=104.1

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh-cC-ceeCCcEEEEeeccCCCCCCC-CCccCCCCCCCCCCccchhhhhhhhcCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV-DT-HELGGSTVVVDRATPKEDDFR-PVGRMSHGGYGAYNAYISAATRYAALGA   80 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~-~~-~~i~gr~i~v~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (234)
                      ......++|++.|.|+..+.+..|++ .. +.+.++.+............. +..+                        
T Consensus       123 ~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~------------------------  178 (285)
T KOG4210|consen  123 LEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTRRGLRPKNKLSR------------------------  178 (285)
T ss_pred             hccccccccceeeccccHHHHHHHHHhhhccccccccccCcccccccccccchhcc------------------------
Confidence            34567899999999999999999995 33 466777665554443321100 0000                        


Q ss_pred             CCccCCCCCCCCCCCCCCCCCCEEE-EeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           81 PTLYDHPGSFYGRGESSQRIGKKIF-VGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~l~-v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                     .......++| |++|+..+++++|+.+|..+|.|..++++  +.++ .++|++|.|.+...+..+
T Consensus       179 ---------------~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~  243 (285)
T KOG4210|consen  179 ---------------LSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLA  243 (285)
T ss_pred             ---------------cccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHH
Confidence                           0022344555 99999999999999999999999999999  5666 999999999999999999


Q ss_pred             Hh-cCCccCCeEeEEEeCCCCCCC
Q 026724          157 SR-RSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       157 ~~-~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      +. ..+.+.++++.+.+..+....
T Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  244 LNDQTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             hhcccCcccCcccccccCCCCccc
Confidence            87 566899999999998877654

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.91  E-value=2.3e-09  Score=83.64  Aligned_cols=128  Identities=23%  Similarity=0.360  Sum_probs=96.7

Q ss_pred             CCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            8 KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      +.-++++|+.|.....-.++-  .++..+.-++|++......++.                               .+.+
T Consensus       137 ~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedP-------------------------------sl~e  185 (290)
T KOG0226|consen  137 QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDP-------------------------------SLAE  185 (290)
T ss_pred             CccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCc-------------------------------cccc
Confidence            567889999988777666665  2455666666655444333221                               1111


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcC
Q 026724           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRS  160 (234)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~  160 (234)
                                 ......+||++.|..+++++.|-..|.+|-.....+++  +.|+ ++||+||.|.+..++..|+  +++
T Consensus       186 -----------w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~g  254 (290)
T KOG0226|consen  186 -----------WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNG  254 (290)
T ss_pred             -----------CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcc
Confidence                       14567899999999999999999999999888777777  4466 9999999999999999998  478


Q ss_pred             CccCCeEeEEEeCCCCC
Q 026724          161 HEICGQQVAIDSATPLD  177 (234)
Q Consensus       161 ~~~~g~~i~v~~a~~~~  177 (234)
                      ..++.+.|++.....++
T Consensus       255 kyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  255 KYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             cccccchhHhhhhhHHh
Confidence            89999999888766554

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.88  E-value=9.3e-09  Score=78.02  Aligned_cols=79  Identities=25%  Similarity=0.476  Sum_probs=67.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhc-CceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRF-GRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~-G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~  171 (234)
                      .....-+||..+|..+.+.+|..+|.+| |.|..+++.  +.|| ++|||||+|++.+.|.-|.  +|..-+.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            5556779999999999999999999988 777888885  6788 9999999999999999997  46668889999988


Q ss_pred             eCCCC
Q 026724          172 SATPL  176 (234)
Q Consensus       172 ~a~~~  176 (234)
                      +-.|.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            87665

>smart00361 RRM_1 RNA recognition motif

Probab=98.87  E-value=3.8e-09  Score=68.32  Aligned_cols=40  Identities=25%  Similarity=0.357  Sum_probs=35.4

Q ss_pred             CCCCCC--CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEE
Q 026724            2 PKDQGS--KAHRGIGFITFASADSVENLMV--DTHELGGSTVVV   41 (234)
Q Consensus         2 ~rD~~t--g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v   41 (234)
                      +.|+.|  +++||||||+|.+.++|.+|+.  ++..+.|+.|.+
T Consensus        26 ~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       26 YIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             EeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            456666  9999999999999999999994  788999999976

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.84  E-value=2.4e-09  Score=81.17  Aligned_cols=45  Identities=27%  Similarity=0.541  Sum_probs=42.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~   45 (234)
                      ||+|+-|+.++|||||.|.+..||+.||  +++.+|+|+.|+|+.|.
T Consensus        45 IPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   45 IPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            7999999999999999999999999999  47889999999999875

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.82  E-value=6.4e-09  Score=80.67  Aligned_cols=71  Identities=32%  Similarity=0.716  Sum_probs=63.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      .++||++||+.+.+.+|+.+|..||.|..|.+.     .+|+||+|++..+|..|+  ++..+|.+..+.|+++....
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-----~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-----NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-----cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            479999999999999999999999999998884     589999999999999998  57889999888888887654

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.76  E-value=2.2e-09  Score=88.20  Aligned_cols=152  Identities=19%  Similarity=0.209  Sum_probs=95.2

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCcc
Q 026724            6 GSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (234)
                      ..|+..|=|||.|+.+++|+.||. +...|.-|.|.+-.+...+-.+-...... . ....           ....+...
T Consensus       201 pdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s-~-pLi~-----------~~~sp~~p  267 (508)
T KOG1365|consen  201 PDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQVLNREVS-E-PLIP-----------GLTSPLLP  267 (508)
T ss_pred             CCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhcc-c-cccC-----------CCCCCCCC
Confidence            358899999999999999999995 45567777777765543222110000000 0 0000           00000000


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCc-eeE--EEee-cCCC-CcceEEEEEcChHHHHHHHhc
Q 026724           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILD--VYVP-KRTG-HRGFGFVTFAEEVVADRVSRR  159 (234)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~--~~~~-~~~~-~~g~afV~f~~~~~a~~A~~~  159 (234)
                      ..    .....+......+|-+++||+..+.++|.++|..|-. |..  |.++ ...| ..|-|||+|.+.++|.+|..+
T Consensus       268 ~~----p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk  343 (508)
T KOG1365|consen  268 GG----PARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQK  343 (508)
T ss_pred             CC----ccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHH
Confidence            00    0011112334678999999999999999999998864 333  5555 5566 889999999999999999754


Q ss_pred             CC--ccCCeEeEEEeCC
Q 026724          160 SH--EICGQQVAIDSAT  174 (234)
Q Consensus       160 ~~--~~~g~~i~v~~a~  174 (234)
                      .|  ....|-|+|--+.
T Consensus       344 ~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  344 CHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             HHHhhcccceEEEeecc
Confidence            33  3347788886553

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.76  E-value=4.1e-08  Score=77.84  Aligned_cols=80  Identities=25%  Similarity=0.391  Sum_probs=69.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      .....+|+|.|||+.++++||+++|..|+.++.+.|. ...+ +.|.|-|.|...++|.+|+.  ++..++|+.|++...
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            3345789999999999999999999999988888888 6667 99999999999999999985  667999999998876


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      .+..
T Consensus       160 ~~~~  163 (243)
T KOG0533|consen  160 SSPS  163 (243)
T ss_pred             cCcc
Confidence            5443

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

Probab=98.75  E-value=6.9e-08  Score=78.26  Aligned_cols=108  Identities=23%  Similarity=0.391  Sum_probs=75.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC--CCCCCCCCccCCCCCCCCCCccchhhhhhh
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP--KEDDFRPVGRMSHGGYGAYNAYISAATRYA   76 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (234)
                      |+.|+.|++++|||||+|.+.++|..|++  ++..|.|++|.|.++..  .........           .   ......
T Consensus       147 ~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~-----------~---~~~~~~  212 (306)
T COG0724         147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNN-----------L---DASFAK  212 (306)
T ss_pred             eeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccc-----------c---chhhhc
Confidence            46788899999999999999999999995  56799999999999754  111100000           0   000000


Q ss_pred             hcCCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee
Q 026724           77 ALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP  134 (234)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~  134 (234)
                                  ...............+++.+++..++..++..+|..++.+..+.+.
T Consensus       213 ------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (306)
T COG0724         213 ------------KLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLP  258 (306)
T ss_pred             ------------cccccccccccccceeeccccccccchhHHHHhccccccceeeecc
Confidence                        0000111124567889999999999999999999999999776665

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.74  E-value=8.1e-09  Score=79.04  Aligned_cols=49  Identities=35%  Similarity=0.584  Sum_probs=44.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ||-|-.++++||||||+|+..|||.+||.  |..+|.||.|+|.+|.|..-
T Consensus        42 iPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   42 IPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             cccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccc
Confidence            57889999999999999999999999994  56699999999999987654

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.70  E-value=1.1e-07  Score=75.41  Aligned_cols=79  Identities=23%  Similarity=0.362  Sum_probs=70.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ..+...+||+|+.+.+|.++++.+|+.||.|..+.|+  +..+ +++|+||+|.+.+.++.|+. ++..|.++.+.|.+.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLK  177 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeee
Confidence            5677899999999999999999999999999988887  5565 89999999999999999985 889999999999887


Q ss_pred             CCC
Q 026724          174 TPL  176 (234)
Q Consensus       174 ~~~  176 (234)
                      +-.
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            655

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.70  E-value=4.9e-07  Score=73.74  Aligned_cols=157  Identities=19%  Similarity=0.205  Sum_probs=100.3

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      |+-||=|.|.|-..|+++-|++  +...|.|+.|+|+.|.-............       ......-.+...++.... +
T Consensus       180 G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~-------k~k~~~~kk~~k~q~k~~-d  251 (382)
T KOG1548|consen  180 GKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKE-------KGKCKDKKKLKKQQQKLL-D  251 (382)
T ss_pred             CCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCccccc-------ccccccHHHHHHHHHhhc-c
Confidence            6789999999999999999994  78889999999998864322111110000       000000001111111100 0


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEeCCC----CCCC-------HHHHHHHHhhcCceeEEEee-cCCCCcceEEEEEcChHHH
Q 026724           86 HPGSFYGRGESSQRIGKKIFVGRLP----QEAT-------AEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVA  153 (234)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~v~nl~----~~~~-------~~~l~~~f~~~G~v~~~~~~-~~~~~~g~afV~f~~~~~a  153 (234)
                      .....  ..+......++|.|.||=    ...+       +++|.+-+++||.|..|.|. +.  +.|.+-|.|.+.++|
T Consensus       252 w~pd~--~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~h--PdGvvtV~f~n~eeA  327 (382)
T KOG1548|consen  252 WRPDR--DDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRH--PDGVVTVSFRNNEEA  327 (382)
T ss_pred             cCCCc--cccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccC--CCceeEEEeCChHHH
Confidence            00000  111224456789999882    2223       45677789999999999887 33  579999999999999


Q ss_pred             HHHH--hcCCccCCeEeEEEeCCCC
Q 026724          154 DRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       154 ~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      ..||  +++..+.||.|.......+
T Consensus       328 ~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  328 DQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHhcCeeecceEEEEEEeCCc
Confidence            9998  5778999999998865443

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.66  E-value=2.5e-07  Score=71.21  Aligned_cols=84  Identities=18%  Similarity=0.249  Sum_probs=65.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee---cCCC-CcceEEEEEcChHHHHHHH--hcCCccC---CeEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTG-HRGFGFVTFAEEVVADRVS--RRSHEIC---GQQV  168 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~---~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~---g~~i  168 (234)
                      ....++|||.+||.++...+|..+|..|--.+.+.|.   +... .+-+|||+|.+..+|.+|+  +++..++   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            3347899999999999999999999998766666555   3333 5689999999999999997  4666554   6789


Q ss_pred             EEEeCCCCCCCCC
Q 026724          169 AIDSATPLDDAGP  181 (234)
Q Consensus       169 ~v~~a~~~~~~~~  181 (234)
                      +|++|+.......
T Consensus       111 hiElAKSNtK~kr  123 (284)
T KOG1457|consen  111 HIELAKSNTKRKR  123 (284)
T ss_pred             EeeehhcCccccc
Confidence            9998876654443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.58  E-value=2.5e-06  Score=70.37  Aligned_cols=124  Identities=17%  Similarity=0.219  Sum_probs=89.3

Q ss_pred             cceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCC
Q 026724           11 RGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDH   86 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (234)
                      +--|.|+|++.+.|++++.    +...|.|+...+.++.++.-.....                                
T Consensus        67 ~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~R~g~--------------------------------  114 (494)
T KOG1456|consen   67 KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIERPGD--------------------------------  114 (494)
T ss_pred             cceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhccCCC--------------------------------
Confidence            3469999999999999992    3557888888888775543211100                                


Q ss_pred             CCCCCCCCCCCCCCCCEEEEe--CCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCc
Q 026724           87 PGSFYGRGESSQRIGKKIFVG--RLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHE  162 (234)
Q Consensus        87 ~~~~~~~~~~~~~~~~~l~v~--nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~  162 (234)
                               ....+...|.+.  |--+.+|-+-|..++...|+|..|.|.+.+  ---|.|+|++.+.|++|-  +|+..
T Consensus       115 ---------es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkn--gVQAmVEFdsv~~AqrAk~alNGAD  183 (494)
T KOG1456|consen  115 ---------ESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKN--GVQAMVEFDSVEVAQRAKAALNGAD  183 (494)
T ss_pred             ---------CCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEecc--ceeeEEeechhHHHHHHHhhccccc
Confidence                     012234445444  445678999999999999999999998543  345899999999999986  56665


Q ss_pred             cC-C-eEeEEEeCCCCC
Q 026724          163 IC-G-QQVAIDSATPLD  177 (234)
Q Consensus       163 ~~-g-~~i~v~~a~~~~  177 (234)
                      |. | ..|+|+||+|..
T Consensus       184 IYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  184 IYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             ccccceeEEEEecCcce
Confidence            43 3 589999999864

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.58  E-value=1.2e-07  Score=75.74  Aligned_cols=56  Identities=16%  Similarity=0.268  Sum_probs=47.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCcc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGR   56 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~   56 (234)
                      ||+|+.||+|||||||+|+++.+..+|.+  .+..|+|+.|.|.+-..+......+.+
T Consensus       133 lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRTvkgW~PRR  190 (335)
T KOG0113|consen  133 LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRTVKGWLPRR  190 (335)
T ss_pred             EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEeccccccccccccc
Confidence            68999999999999999999999999995  578999999999987766555544443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.54  E-value=3.8e-08  Score=75.37  Aligned_cols=75  Identities=15%  Similarity=0.290  Sum_probs=63.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC--CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~--~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      .....+|||+||...++|+.|.++|-+-|+|..|.|++...  .| ||||.|.++.+..-|+  +++..+.++.+.|.+-
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            45678999999999999999999999999999999983333  45 9999999999999886  5888888877777653

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.53  E-value=2.5e-07  Score=81.76  Aligned_cols=78  Identities=23%  Similarity=0.386  Sum_probs=67.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cC----CC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KR----TG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVA  169 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~----~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~  169 (234)
                      ++.+++|||+||++.++++.|...|..||+|..|+|+ ..    .. .+-|+||.|.+..+|++|+.  ++..+....++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            5678899999999999999999999999999999998 11    12 57899999999999999984  67788999999


Q ss_pred             EEeCCC
Q 026724          170 IDSATP  175 (234)
Q Consensus       170 v~~a~~  175 (234)
                      +-|+++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999843

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.50  E-value=1.2e-07  Score=71.99  Aligned_cols=46  Identities=13%  Similarity=0.239  Sum_probs=40.0

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      -|++.||.|||||||+|+++|.|+-|-+  |+..|.++-|.|.+--+.
T Consensus        83 sRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   83 SRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             ecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            4789999999999999999999999984  677889999999876543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.50  E-value=3.8e-06  Score=70.09  Aligned_cols=72  Identities=14%  Similarity=0.283  Sum_probs=63.6

Q ss_pred             CCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          101 GKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       101 ~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ...|.|.||.. .+|.+.|..+|.-||.|..|.|...  .+--|.|+|.+...|+-|+  ++++.+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~n--kkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYN--KKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeec--CCcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57888999965 5799999999999999999999943  2467999999999999998  58999999999999886

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.44  E-value=7.5e-06  Score=67.65  Aligned_cols=143  Identities=15%  Similarity=0.077  Sum_probs=87.9

Q ss_pred             cceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCc-cchhhhhhhhcCCCCccCCC
Q 026724           11 RGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNA-YISAATRYAALGAPTLYDHP   87 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   87 (234)
                      -|-|.|++.|..+.++|+  +|+..+.|.+|.|+.+...--..-..- ...++...... ..+...|+..........  
T Consensus       325 ~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pf-lLpDgSpSfKdys~SkNnRFssp~qAsKNr--  401 (494)
T KOG1456|consen  325 PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPF-LLPDGSPSFKDYSGSKNNRFSSPEQASKNR--  401 (494)
T ss_pred             cceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCce-ecCCCCcchhhcccccccccCChhHhhccc--
Confidence            478999999999999999  578888999999987654322211000 01111111111 111122221111111111  


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCc-eeEEEeecC-CCCcceEEEEEcChHHHHHHHh--cCCcc
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPKR-TGHRGFGFVTFAEEVVADRVSR--RSHEI  163 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~~~-~~~~g~afV~f~~~~~a~~A~~--~~~~~  163 (234)
                               -..+++.|..-|.|..+||+.|.++|..-.. -.+|+|... +....-+.++|++.++|..||.  |...|
T Consensus       402 ---------Iq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~kserSssGllEfe~~s~Aveal~~~NH~pi  472 (494)
T KOG1456|consen  402 ---------IQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLKSERSSSGLLEFENKSDAVEALMKLNHYPI  472 (494)
T ss_pred             ---------ccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeecccccccccceeeeehHHHHHHHHHHhccccc
Confidence                     1456889999999999999999999976654 355666621 2233457999999999999984  44444


Q ss_pred             CC
Q 026724          164 CG  165 (234)
Q Consensus       164 ~g  165 (234)
                      .+
T Consensus       473 ~~  474 (494)
T KOG1456|consen  473 EG  474 (494)
T ss_pred             cC
Confidence            43

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.44  E-value=5.7e-08  Score=72.37  Aligned_cols=47  Identities=17%  Similarity=0.338  Sum_probs=42.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~   47 (234)
                      |+||+.||+|+||||+.|++.....-|+  .|+..|.||.|+|......
T Consensus        67 LiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Y  115 (219)
T KOG0126|consen   67 LIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNY  115 (219)
T ss_pred             EEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccc
Confidence            6899999999999999999999999999  4688999999999876544

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.44  E-value=2.3e-07  Score=80.02  Aligned_cols=70  Identities=26%  Similarity=0.447  Sum_probs=61.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVA  169 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~  169 (234)
                      +....+|+|-|||..+++++|+.+|+.||+|+.|+..+.  .++..||+|-|..+|+.|++  +..++.|+.|+
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            566789999999999999999999999999999665433  57999999999999999984  67788888877

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.39  E-value=1.6e-06  Score=70.79  Aligned_cols=78  Identities=17%  Similarity=0.368  Sum_probs=66.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE--------EEee-cCCC-CcceEEEEEcChHHHHHHH--hcCCccCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVP-KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICG  165 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~-~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g  165 (234)
                      ......|||.|||.++|.+++.++|++||.|..        |.|- ...| .+|=|.+.|...+++.-|+  ++...|.|
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            345667999999999999999999999998743        4555 4446 8999999999999999997  57789999


Q ss_pred             eEeEEEeCCC
Q 026724          166 QQVAIDSATP  175 (234)
Q Consensus       166 ~~i~v~~a~~  175 (234)
                      +.|+|+.|+=
T Consensus       211 ~~~rVerAkf  220 (382)
T KOG1548|consen  211 KKLRVERAKF  220 (382)
T ss_pred             cEEEEehhhh
Confidence            9999998863

>PF13893 RRM_5: RNA recognition motif

Probab=98.38  E-value=9.6e-07  Score=54.25  Aligned_cols=34  Identities=26%  Similarity=0.556  Sum_probs=31.6

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeec
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a   44 (234)
                      +++|||+|.+.++|++|+.  ++..+.|++|+|.+|
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            6999999999999999995  788999999999985

(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 ....

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.36  E-value=2.9e-06  Score=70.23  Aligned_cols=134  Identities=21%  Similarity=0.200  Sum_probs=89.5

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            7 SKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      .|+-.|.|.|.|.|.|.-+.|++ ..|.+.++.|.|-.+....--.-..                               
T Consensus        98 qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~f~~iag-------------------------------  146 (508)
T KOG1365|consen   98 QGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEEFLKIAG-------------------------------  146 (508)
T ss_pred             hhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchhheEecC-------------------------------
Confidence            35667899999999999999997 4778899999998776432111000                               


Q ss_pred             CCCCCCCCCCC-CCCCCCEEEEeCCCCCCCHHHHHHHHhhcC----ceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh
Q 026724           86 HPGSFYGRGES-SQRIGKKIFVGRLPQEATAEDLRRYFSRFG----RILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus        86 ~~~~~~~~~~~-~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G----~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~  158 (234)
                        ..+...... ....--.|-+++||+++++.|+.++|.+--    -++.|.++ +..+ ..|-|||.|..+++|+.||.
T Consensus       147 --g~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~  224 (508)
T KOG1365|consen  147 --GTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR  224 (508)
T ss_pred             --CccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH
Confidence              000000000 012234567789999999999999996322    33455555 5455 89999999999999999996


Q ss_pred             cCC-ccCCeEeEEEeC
Q 026724          159 RSH-EICGQQVAIDSA  173 (234)
Q Consensus       159 ~~~-~~~g~~i~v~~a  173 (234)
                      +.. .|.-|-|++-.+
T Consensus       225 khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  225 KHRQNIGQRYIELFRS  240 (508)
T ss_pred             HHHHHHhHHHHHHHHH
Confidence            544 444445555433

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.28  E-value=6.7e-06  Score=67.63  Aligned_cols=81  Identities=21%  Similarity=0.364  Sum_probs=68.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE--------EEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~  164 (234)
                      .....+|||-+||..+++++|.++|.+++.|..        |.|-  +.|+ .|+-|.|+|++...|+.||.  +...++
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            455678999999999999999999999998843        2222  6677 99999999999999999985  677999


Q ss_pred             CeEeEEEeCCCCCC
Q 026724          165 GQQVAIDSATPLDD  178 (234)
Q Consensus       165 g~~i~v~~a~~~~~  178 (234)
                      +..|+|.+|..+..
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999999876653

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.27  E-value=9.2e-07  Score=76.09  Aligned_cols=49  Identities=20%  Similarity=0.457  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |+-|+.||++|||||++|.+.++|+.|+.  |+.++.||+|+|.|+.....
T Consensus        50 ~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~  100 (435)
T KOG0108|consen   50 LVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKN  100 (435)
T ss_pred             ecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccch
Confidence            46799999999999999999999999995  68899999999999876544

>smart00360 RRM RNA recognition motif

Probab=98.27  E-value=1.6e-06  Score=54.91  Aligned_cols=41  Identities=24%  Similarity=0.524  Sum_probs=34.8

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEe
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVD   42 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~   42 (234)
                      ++++.+++++|||||+|.+.++|.+|+.  ++..+.++.|.|.
T Consensus        29 ~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       29 VRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             EeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            4556688999999999999999999995  4678899998873

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.27  E-value=1.3e-06  Score=56.20  Aligned_cols=38  Identities=21%  Similarity=0.483  Sum_probs=32.7

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEE
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVV   40 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~   40 (234)
                      +++++ ++++|+|||+|.+.++|.+|+.  +++.|+|+.|+
T Consensus        31 ~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   31 IKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             Eeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            45666 8999999999999999999995  45899999884

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 ....

>PF00076 RRM_1: RNA recognition motif

Probab=98.25  E-value=1.2e-06  Score=55.96  Aligned_cols=35  Identities=20%  Similarity=0.480  Sum_probs=31.8

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEE
Q 026724            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVV   40 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~   40 (234)
                      .++.++|||||+|++.++|++|++  +++.|.|+.|+
T Consensus        34 ~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   34 SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            578999999999999999999995  68899999885

(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 ....

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.24  E-value=1.2e-06  Score=79.09  Aligned_cols=106  Identities=18%  Similarity=0.274  Sum_probs=83.7

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCcc
Q 026724            6 GSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (234)
                      .+++-||+|+|+|.+++++.+||. +...+.|                                                
T Consensus       704 n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g------------------------------------------------  735 (881)
T KOG0128|consen  704 NEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG------------------------------------------------  735 (881)
T ss_pred             hccccccceeeEeecCCchhhhhhhhhhhhhh------------------------------------------------
Confidence            568899999999999999999995 2222222                                                


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHhc--C
Q 026724           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSRR--S  160 (234)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~~--~  160 (234)
                                      ...|+|.|+|+..|.++|+.++..+|.+++++++ ...+ ++|.+||.|.+..++.+++..  .
T Consensus       736 ----------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~  799 (881)
T KOG0128|consen  736 ----------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDV  799 (881)
T ss_pred             ----------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchh
Confidence                            1358999999999999999999999999998877 3344 999999999999999998753  3


Q ss_pred             CccCCeEeEEEeCCC
Q 026724          161 HEICGQQVAIDSATP  175 (234)
Q Consensus       161 ~~~~g~~i~v~~a~~  175 (234)
                      ..+.-+.+.|..+.|
T Consensus       800 ~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  800 AGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhhcCccccccCC
Confidence            344555566666555

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.24  E-value=2.2e-05  Score=67.45  Aligned_cols=75  Identities=27%  Similarity=0.385  Sum_probs=60.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHh-hcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhc-CCcc----CCeEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFS-RFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRR-SHEI----CGQQV  168 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~-~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~-~~~~----~g~~i  168 (234)
                      -.+.++||||+||.-++.++|..+|+ -||.|..+-|-  .+-+ ++|-|=|+|.+..+-.+||.. ...|    -.++|
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~KRV  446 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDKRV  446 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccceee
Confidence            56789999999999999999999998 69999998887  3455 999999999999999999853 2222    23466


Q ss_pred             EEEe
Q 026724          169 AIDS  172 (234)
Q Consensus       169 ~v~~  172 (234)
                      +|+-
T Consensus       447 EIkP  450 (520)
T KOG0129|consen  447 EIKP  450 (520)
T ss_pred             eecc
Confidence            6653

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=98.23  E-value=9.1e-07  Score=71.75  Aligned_cols=41  Identities=20%  Similarity=0.455  Sum_probs=36.7

Q ss_pred             CCccceEEEEEcCHHHHHHHHhc--CceeCCcEEEEeeccCCC
Q 026724            8 KAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~~--~~~i~gr~i~v~~a~~~~   48 (234)
                      .-|||||||+|++.+||++|-++  +..|.||+|+|+.|..+-
T Consensus       133 RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  133 RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARV  175 (376)
T ss_pred             CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhh
Confidence            45999999999999999999964  669999999999998764

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.19  E-value=6.6e-06  Score=72.91  Aligned_cols=159  Identities=13%  Similarity=0.054  Sum_probs=95.9

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAP   81 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (234)
                      +|+..+--.|-++|+|....++++|+.. ...+-.|.+.|..+........+............          ..+..+
T Consensus       344 ~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~----------~~hg~p  413 (944)
T KOG4307|consen  344 ENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQ----------NNHGRP  413 (944)
T ss_pred             hhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCCccccccCccccccCCCCccc----------ccCCCC
Confidence            3444343478999999999999999964 44556788877655433221111110000000000          001111


Q ss_pred             CccCCCCCCCCC-CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEee-cCCC-CcceEEEEEcChHHHHHHH
Q 026724           82 TLYDHPGSFYGR-GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVP-KRTG-HRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        82 ~~~~~~~~~~~~-~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~-~~~~-~~g~afV~f~~~~~a~~A~  157 (234)
                      ...+......+. .........+|||..||..+++.++.++|...-.|++ |.|. -.++ .++.|||+|..++++..|+
T Consensus       414 ~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~  493 (944)
T KOG4307|consen  414 IAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTAS  493 (944)
T ss_pred             CCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhh
Confidence            111100000000 1122456789999999999999999999988777776 6665 3344 7899999999988888886


Q ss_pred             h--cCCccCCeEeEEE
Q 026724          158 R--RSHEICGQQVAID  171 (234)
Q Consensus       158 ~--~~~~~~g~~i~v~  171 (234)
                      +  ..+.+..+.|+|.
T Consensus       494 ~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  494 SVKTKFYPGHRIIRVD  509 (944)
T ss_pred             hcccccccCceEEEee
Confidence            4  3446666777775

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.16  E-value=1.9e-06  Score=61.31  Aligned_cols=47  Identities=19%  Similarity=0.299  Sum_probs=42.2

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      -|+.||-.||||.|+|++.++|++||  +|+..|.+++|.|.|+..+..
T Consensus       106 LDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~gp  154 (170)
T KOG0130|consen  106 LDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKGP  154 (170)
T ss_pred             cccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecCC
Confidence            47889999999999999999999999  478899999999999976544

>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=98.15  E-value=1.6e-05  Score=52.01  Aligned_cols=68  Identities=18%  Similarity=0.464  Sum_probs=44.6

Q ss_pred             CEEEEeCCCCCCCHHHH----HHHHhhcC-ceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724          102 KKIFVGRLPQEATAEDL----RRYFSRFG-RILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l----~~~f~~~G-~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ..|+|.|||.+.+...|    ++++..|| .|..|       ..+.|+|.|.+.+.|.+|.+  ++..+.|++|.|.+..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            36999999999987664    55666776 56555       24789999999999999984  6779999999999984


Q ss_pred             CC
Q 026724          175 PL  176 (234)
Q Consensus       175 ~~  176 (234)
                      ..
T Consensus        76 ~~   77 (90)
T PF11608_consen   76 KN   77 (90)
T ss_dssp             -S
T ss_pred             Cc
Confidence            33

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

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

Probab=98.14  E-value=2.8e-05  Score=53.12  Aligned_cols=74  Identities=20%  Similarity=0.343  Sum_probs=55.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhc--CceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCcc----CCeEeEE
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRF--GRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEI----CGQQVAI  170 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~----~g~~i~v  170 (234)
                      ++|.|.|||...|.++|.+++...  |....+.++  -.+. +.|||||.|.+++.|.+-..  ++..+    ..+.+.|
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            589999999999999999988653  455556666  3345 89999999999999988653  44433    3456788


Q ss_pred             EeCCC
Q 026724          171 DSATP  175 (234)
Q Consensus       171 ~~a~~  175 (234)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88764

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

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=98.11  E-value=2.2e-06  Score=63.66  Aligned_cols=41  Identities=22%  Similarity=0.465  Sum_probs=36.0

Q ss_pred             CccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCC
Q 026724            9 AHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ..-|||||+|+++.||+.|+  +++..|+|..|+|+.+.-...
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            46799999999999999999  689999999999998875443

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.05  E-value=7.1e-06  Score=65.57  Aligned_cols=44  Identities=16%  Similarity=0.324  Sum_probs=37.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.   ++|||||+|+++++|+.|| +++..|.|+.|.|.++...
T Consensus        36 I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120         36 MQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             EeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            355553   5799999999999999999 5889999999999988644

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.03  E-value=2e-06  Score=67.55  Aligned_cols=48  Identities=19%  Similarity=0.411  Sum_probs=42.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++||+.|++|+||+||.|.+++|+..|+  +++..++.++|.++.+.-+.
T Consensus       222 viRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  222 VIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             ccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            5799999999999999999999999999  47889999999887665443

>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=98.00  E-value=9.6e-06  Score=56.53  Aligned_cols=68  Identities=22%  Similarity=0.382  Sum_probs=41.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhc-------CCccCCeEeEEEe
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR-------SHEICGQQVAIDS  172 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-------~~~~~g~~i~v~~  172 (234)
                      +.|+|.+++..++.++|+++|++||.|..|.+.+.   -..|||.|.+.++|+.|+..       ...|.+..+.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G---~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG---DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT----SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC---CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            46889999999999999999999999999988743   24799999999999999742       2355665555543

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

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=97.98  E-value=9e-06  Score=57.39  Aligned_cols=44  Identities=20%  Similarity=0.304  Sum_probs=39.9

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      -|+.|...-|||||+|.+.++|+.||.  ++..|+.++|+|.|..-
T Consensus        70 Ldr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   70 LDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             cccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecccc
Confidence            478899999999999999999999995  78999999999998653

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

Probab=97.90  E-value=4.7e-05  Score=46.07  Aligned_cols=52  Identities=25%  Similarity=0.500  Sum_probs=42.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~  157 (234)
                      +.|-|.+.+.+..+.. ..+|..||+|..+.+..   ...+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~v-l~~F~~fGeI~~~~~~~---~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEV-LEHFASFGEIVDIYVPE---STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHH-HHHHHhcCCEEEEEcCC---CCcEEEEEECCHHHHHhhC
Confidence            4677888887777554 45888999999998863   2578999999999999985

>smart00362 RRM_2 RNA recognition motif

Probab=97.90  E-value=2.4e-05  Score=49.52  Aligned_cols=35  Identities=26%  Similarity=0.576  Sum_probs=30.8

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEe
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVD   42 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~   42 (234)
                      +.++|+|||+|.+.++|++|++  ++..+.++.|.|+
T Consensus        36 ~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       36 GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            6789999999999999999995  5678999998773

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.86  E-value=1.1e-05  Score=66.36  Aligned_cols=49  Identities=18%  Similarity=0.278  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ||||+.||.|--||||+|++.+++++|.  |++..|+.+.|.|.++.+-..
T Consensus       271 VIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVsk  321 (479)
T KOG0415|consen  271 VIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVSK  321 (479)
T ss_pred             EEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhhh
Confidence            5899999999999999999999999999  578899999999999865433

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.77  E-value=9e-05  Score=60.88  Aligned_cols=71  Identities=18%  Similarity=0.315  Sum_probs=54.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcC--ceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      ...++||+||-|.+|++||.+.+...|  .+.++++.  +.++ +||||.|...+..+.++.+  +-..+|.|+.-.|
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            345799999999999999999888766  35566666  6677 9999999999887777765  3455777764333

>PLN03213 repressor of silencing 3; Provisional

Probab=97.68  E-value=4.4e-05  Score=65.43  Aligned_cols=40  Identities=18%  Similarity=0.401  Sum_probs=35.2

Q ss_pred             CCCCCccceEEEEEcCH--HHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            5 QGSKAHRGIGFITFASA--DSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~--e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      +.||  ||||||+|.+.  +++.+||  +++..+.|+.|+|..|.+
T Consensus        44 RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         44 RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            5577  99999999987  6789999  478999999999999865

>PLN03121 nucleic acid binding protein; Provisional

Probab=97.67  E-value=6.8e-05  Score=59.16  Aligned_cols=43  Identities=14%  Similarity=0.220  Sum_probs=36.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~   46 (234)
                      |++|   +.+++||||+|+++++|+.|| +++..|.+++|.|..+..
T Consensus        37 I~~D---~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121         37 IIRS---GEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             EecC---CCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            4566   456689999999999999999 589999999999987654

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=97.66  E-value=0.00011  Score=46.65  Aligned_cols=39  Identities=26%  Similarity=0.582  Sum_probs=32.0

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEee
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDR   43 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~   43 (234)
                      ++.+ .++|+|||+|.+.++|..|+.  ++..+.++.|.|.+
T Consensus        34 ~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          34 DKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            3443 679999999999999999995  46678999998863

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).

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.60  E-value=5.8e-06  Score=69.32  Aligned_cols=117  Identities=15%  Similarity=0.237  Sum_probs=92.8

Q ss_pred             cceEEEEEcCHHHHHHHHhc---CceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCC
Q 026724           11 RGIGFITFASADSVENLMVD---THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~~---~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (234)
                      -|||||...+...|.+|++.   ..++.|+.+.|....++..                                      
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq--------------------------------------   78 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ--------------------------------------   78 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH--------------------------------------
Confidence            48999999999999999963   3489999999988876643                                      


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCC
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICG  165 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g  165 (234)
                                  .++++-|.|+|+...++.|..++.+||.+..|..+...--....-|+|.+.+.+..||  ++++.+..
T Consensus        79 ------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en  146 (584)
T KOG2193|consen   79 ------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLEN  146 (584)
T ss_pred             ------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhh
Confidence                        2456889999999999999999999999999877621112333457888888999998  46778889


Q ss_pred             eEeEEEeCCCCC
Q 026724          166 QQVAIDSATPLD  177 (234)
Q Consensus       166 ~~i~v~~a~~~~  177 (234)
                      ..++|.|-....
T Consensus       147 ~~~k~~YiPdeq  158 (584)
T KOG2193|consen  147 QHLKVGYIPDEQ  158 (584)
T ss_pred             hhhhcccCchhh
Confidence            999998865443

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.55  E-value=0.00019  Score=56.68  Aligned_cols=73  Identities=27%  Similarity=0.413  Sum_probs=57.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHhc------CCccCCeEeEEEeC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSRR------SHEICGQQVAIDSA  173 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~~------~~~~~g~~i~v~~a  173 (234)
                      ..|||.||+..++-+.|.+.|+.||.|....+. .+.+ ..+-++|.|...-.|.+|+..      +....++++-|...
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            579999999999999999999999999775554 5555 788899999999888888632      12666777666554


Q ss_pred             C
Q 026724          174 T  174 (234)
Q Consensus       174 ~  174 (234)
                      .
T Consensus       112 e  112 (275)
T KOG0115|consen  112 E  112 (275)
T ss_pred             h
Confidence            3

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.55  E-value=2e-05  Score=60.64  Aligned_cols=94  Identities=26%  Similarity=0.403  Sum_probs=71.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++++. ++.| ||||.|+++-.+.-|+  +|+..|.++.|.|++-                                  
T Consensus        41 ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r----------------------------------   84 (267)
T KOG4454|consen   41 IPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR----------------------------------   84 (267)
T ss_pred             CCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccc----------------------------------
Confidence            344444 6677 9999999999999999  4888888888877532                                  


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeC----CCCCCCHHHHHHHHhhcCceeEEEeec-CCC-CcceEEEEEcChHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGR----LPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVV  152 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~n----l~~~~~~~~l~~~f~~~G~v~~~~~~~-~~~-~~g~afV~f~~~~~  152 (234)
                                                 .|+    |...++++.+.+.|+.-+.+..+++.. ..+ ++.+.|+++.....
T Consensus        85 ---------------------------~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~  137 (267)
T KOG4454|consen   85 ---------------------------CGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCA  137 (267)
T ss_pred             ---------------------------cCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhc
Confidence                                       223    556788999999999999999999982 234 88999998876655


Q ss_pred             HHHHH
Q 026724          153 ADRVS  157 (234)
Q Consensus       153 a~~A~  157 (234)
                      .-.++
T Consensus       138 ~P~~~  142 (267)
T KOG4454|consen  138 VPFAL  142 (267)
T ss_pred             CcHHh
Confidence            55554

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.52  E-value=0.00046  Score=59.59  Aligned_cols=60  Identities=30%  Similarity=0.584  Sum_probs=47.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee----cCCC--Ccc---eEEEEEcChHHHHHHHh
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP----KRTG--HRG---FGFVTFAEEVVADRVSR  158 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~----~~~~--~~g---~afV~f~~~~~a~~A~~  158 (234)
                      ..-+++|||++||++++|+.|...|..||.+. |.++    ....  ++|   |+|+.|+++.++..-|.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~  324 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLS  324 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHH
Confidence            55678999999999999999999999999864 4444    1111  567   99999999887776553

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.50  E-value=0.0001  Score=67.33  Aligned_cols=116  Identities=19%  Similarity=0.341  Sum_probs=86.3

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      +.---||||.|.+.+.+-.|+.  .+..|..-.+++.+-.++                                      
T Consensus       410 ~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~k--------------------------------------  451 (975)
T KOG0112|consen  410 KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQPK--------------------------------------  451 (975)
T ss_pred             CcccchhhhhhhccccCcccchhhcCCccccCcccccccccc--------------------------------------
Confidence            3344588999999888888873  344444334444433221                                      


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCcc
Q 026724           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEI  163 (234)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~  163 (234)
                                  ....+.+||++|..++....|...|..||.|..|.+-..   .-|++|.|++...++.|+.  .+..|
T Consensus       452 ------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg---q~yayi~yes~~~aq~a~~~~rgap~  516 (975)
T KOG0112|consen  452 ------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG---QPYAYIQYESPPAAQAATHDMRGAPL  516 (975)
T ss_pred             ------------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC---CcceeeecccCccchhhHHHHhcCcC
Confidence                        345788999999999999999999999999999888632   4699999999999999974  45555


Q ss_pred             CC--eEeEEEeCCCC
Q 026724          164 CG--QQVAIDSATPL  176 (234)
Q Consensus       164 ~g--~~i~v~~a~~~  176 (234)
                      .+  +.+.|.++.+.
T Consensus       517 G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  517 GGPPRRLRVDLASPP  531 (975)
T ss_pred             CCCCcccccccccCC
Confidence            54  57888888654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.45  E-value=0.00051  Score=61.37  Aligned_cols=70  Identities=20%  Similarity=0.326  Sum_probs=59.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCcee-EEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRIL-DVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~-~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      .|-|.|+|++++-+||.++|..|-.+. +|.+. .+.+ ..|-|.|.|++.++|.+|.+  +...|..++|.|.+
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            788999999999999999999997664 45555 5566 89999999999999999974  67799999988764

>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=0.00083  Score=46.18  Aligned_cols=74  Identities=19%  Similarity=0.328  Sum_probs=50.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cC---------CCCcceEEEEEcChHHHHHHH-hcCCccCCeE-
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KR---------TGHRGFGFVTFAEEVVADRVS-RRSHEICGQQ-  167 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~---------~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~-  167 (234)
                      ....|.|-+.|+. ....|.++|++||.|.+..-. +.         .....+-.|+|+++.+|.+|| +|+..|.|.. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            3566888899988 455677889999999877511 10         013578999999999999999 4788888864 


Q ss_pred             eEEEeCC
Q 026724          168 VAIDSAT  174 (234)
Q Consensus       168 i~v~~a~  174 (234)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4566654

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.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.42  E-value=0.00045  Score=56.68  Aligned_cols=77  Identities=21%  Similarity=0.384  Sum_probs=59.9

Q ss_pred             CCCCEEEEeCCCCCCCHHH----H--HHHHhhcCceeEEEeecCC-C---Ccce--EEEEEcChHHHHHHHh--cCCccC
Q 026724           99 RIGKKIFVGRLPQEATAED----L--RRYFSRFGRILDVYVPKRT-G---HRGF--GFVTFAEEVVADRVSR--RSHEIC  164 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~----l--~~~f~~~G~v~~~~~~~~~-~---~~g~--afV~f~~~~~a~~A~~--~~~~~~  164 (234)
                      ....-+||-+||+.+..++    |  .++|.+||.|..|.|-+.+ .   --+.  .||+|.+.|+|..||.  ++..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            3456789999999886655    3  5899999999999887332 1   1122  3999999999999984  688999


Q ss_pred             CeEeEEEeCCC
Q 026724          165 GQQVAIDSATP  175 (234)
Q Consensus       165 g~~i~v~~a~~  175 (234)
                      ||.|+..|...
T Consensus       192 Gr~lkatYGTT  202 (480)
T COG5175         192 GRVLKATYGTT  202 (480)
T ss_pred             CceEeeecCch
Confidence            99999988754

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.29  E-value=0.0012  Score=55.77  Aligned_cols=60  Identities=22%  Similarity=0.390  Sum_probs=51.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecC-------CC--C-------cceEEEEEcChHHHHHHH
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------TG--H-------RGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~-------~~--~-------~g~afV~f~~~~~a~~A~  157 (234)
                      ..++++|.+-|||.+-.-+.|.++|..+|.|+.|+|.+.       .+  +       +-+|+|+|+..+.|.+|.
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            457899999999999999999999999999999999722       12  2       457999999999999996

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

Probab=97.26  E-value=0.00047  Score=47.08  Aligned_cols=46  Identities=17%  Similarity=0.298  Sum_probs=36.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCcee----CCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHEL----GGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i----~gr~i~v~~a~~   46 (234)
                      ||.|..|+.+.|||||.|.++++|.+...  ++..+    ..+...|.+|.-
T Consensus        35 LPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAri   86 (97)
T PF04059_consen   35 LPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYARI   86 (97)
T ss_pred             eeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhHh
Confidence            68899999999999999999999999885  45444    345567777653

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

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.21  E-value=0.00038  Score=55.45  Aligned_cols=46  Identities=26%  Similarity=0.438  Sum_probs=41.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.++.+||||||+|.+.+.+++|+. ++..|.++.|.|.+..-
T Consensus       133 i~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r~  179 (231)
T KOG4209|consen  133 VPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKRT  179 (231)
T ss_pred             eeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeeee
Confidence            57899999999999999999999999995 88999999999987643

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.08  E-value=1.5e-05  Score=72.13  Aligned_cols=107  Identities=25%  Similarity=0.213  Sum_probs=76.8

Q ss_pred             eEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCCCCCC
Q 026724           13 IGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFY   91 (234)
Q Consensus        13 ~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (234)
                      ++++.++...+++.|.. .+..+.++.+.|..+.++.......                                     
T Consensus       616 ~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~~~~~~~~k-------------------------------------  658 (881)
T KOG0128|consen  616 QQQKVQSKHGSAESATVPAGGALANRSAAVGLADAEEKEENFK-------------------------------------  658 (881)
T ss_pred             hhhhhhccccchhhcccccccccCCccccCCCCCchhhhhccC-------------------------------------
Confidence            66777777777777773 4556666666666555443211110                                     


Q ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH
Q 026724           92 GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        92 ~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~  157 (234)
                       ..+.......++||.||+..+.+.+|...|..++.+..+.+.  ..++ .+|+|+|+|...+++.+||
T Consensus       659 -vs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV  726 (881)
T KOG0128|consen  659 -VSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAV  726 (881)
T ss_pred             -cCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhh
Confidence             000012345789999999999999999999999988777665  5666 8999999999999999987

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.05  E-value=0.0012  Score=45.15  Aligned_cols=42  Identities=17%  Similarity=0.290  Sum_probs=36.8

Q ss_pred             CCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCC
Q 026724            6 GSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~   47 (234)
                      .|...||-|||.|++..||.+|+  +++..++++.+.|-+..+.
T Consensus        52 ~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   52 NTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             CccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            46678999999999999999999  4788999999999887653

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.96  E-value=0.0051  Score=44.96  Aligned_cols=74  Identities=18%  Similarity=0.192  Sum_probs=51.1

Q ss_pred             CCCCEEEEeCCCC-----CC-CH---HHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeEe
Q 026724           99 RIGKKIFVGRLPQ-----EA-TA---EDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQV  168 (234)
Q Consensus        99 ~~~~~l~v~nl~~-----~~-~~---~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i  168 (234)
                      ++..+|.|.=+.+     .. .+   .+|.+.|..||.+.-|+++.     +.-+|+|.+-++|.+|+ +++..++|+.|
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~-----~~mwVTF~dg~sALaals~dg~~v~g~~l   99 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG-----DTMWVTFRDGQSALAALSLDGIQVNGRTL   99 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET-----TCEEEEESSCHHHHHHHHGCCSEETTEEE
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC-----CeEEEEECccHHHHHHHccCCcEECCEEE
Confidence            3466777765541     12 22   26778888999998888874     35799999999999999 58999999999


Q ss_pred             EEEeCCCCC
Q 026724          169 AIDSATPLD  177 (234)
Q Consensus       169 ~v~~a~~~~  177 (234)
                      +|+...|..
T Consensus       100 ~i~LKtpdW  108 (146)
T PF08952_consen  100 KIRLKTPDW  108 (146)
T ss_dssp             EEEE-----
T ss_pred             EEEeCCccH
Confidence            999876643

; PDB: 1UFW_A 2DNR_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.90  E-value=0.0011  Score=55.45  Aligned_cols=71  Identities=13%  Similarity=0.229  Sum_probs=56.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec---CCC---CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEe
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTG---HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDS  172 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~---~~~---~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~  172 (234)
                      ..|.|.||.+.+|.++++.+|...|.|.++.|..   +..   ..-.|||.|.+...+..|. +....+-++.|.|..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEe
Confidence            3799999999999999999999999999998873   211   4568999999999988884 555566666665553

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.67  E-value=0.003  Score=55.33  Aligned_cols=73  Identities=21%  Similarity=0.419  Sum_probs=54.9

Q ss_pred             CCCCEEEEeCCCCCC------CHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccC-CeE
Q 026724           99 RIGKKIFVGRLPQEA------TAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEIC-GQQ  167 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~------~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~-g~~  167 (234)
                      .-...|+|.|+|---      -..-|..+|+++|+|..+.++ ...+ .+||.|++|.+..+|+.|++  +++.|+ .+.
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            346789999998532      234567899999999999888 4434 99999999999999999995  555444 445


Q ss_pred             eEEE
Q 026724          168 VAID  171 (234)
Q Consensus       168 i~v~  171 (234)
                      ..|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            5554

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=96.65  E-value=0.0046  Score=41.31  Aligned_cols=70  Identities=19%  Similarity=0.277  Sum_probs=45.7

Q ss_pred             EEEEEcCHHHHHHHHhc-Cc--eeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCCCCC
Q 026724           14 GFITFASADSVENLMVD-TH--ELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSF   90 (234)
Q Consensus        14 aFV~F~~~e~A~~Al~~-~~--~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (234)
                      |.|+|++++-|++.+.. .|  .+++..+.|...--.......-.                                   
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~q-----------------------------------   45 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQ-----------------------------------   45 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEE-----------------------------------
Confidence            68999999999999964 34  56677766653311111000000                                   


Q ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHH
Q 026724           91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYF  122 (234)
Q Consensus        91 ~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f  122 (234)
                          .......++|-|.|||...++++|++.+
T Consensus        46 ----v~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen   46 ----VFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             ----EEEcccCCEEEEeCCCCCCChhhheeeE
Confidence                0014457899999999999999998753

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.58  E-value=0.0015  Score=51.63  Aligned_cols=68  Identities=24%  Similarity=0.463  Sum_probs=53.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CC---------CCc----ceEEEEEcChHHHHHHH--hcCCc
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RT---------GHR----GFGFVTFAEEVVADRVS--RRSHE  162 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~---------~~~----g~afV~f~~~~~a~~A~--~~~~~  162 (234)
                      ..-.||+++||+.++..-|+++|++||.|-.|.|.+  .+         +++    --++|+|.+...|..+.  +|+..
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            456799999999999999999999999999988872  22         122    23689999999988864  67777


Q ss_pred             cCCeE
Q 026724          163 ICGQQ  167 (234)
Q Consensus       163 ~~g~~  167 (234)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            77764

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.57  E-value=0.0077  Score=48.70  Aligned_cols=59  Identities=14%  Similarity=0.131  Sum_probs=46.5

Q ss_pred             HHHHHHHHhhcCceeEEEeecCCC----CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724          115 AEDLRRYFSRFGRILDVYVPKRTG----HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus       115 ~~~l~~~f~~~G~v~~~~~~~~~~----~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      ++++++.+++||.|..|.|....+    -.---||+|+..++|.+|+  +++..|.||.+...|-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            457788999999999988771111    2234699999999999997  6888999999887764

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

Probab=96.42  E-value=0.027  Score=37.02  Aligned_cols=52  Identities=25%  Similarity=0.323  Sum_probs=38.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~  157 (234)
                      .....||. +|..+...||.++|+.||.|. |..+.+    .-|||...+.+.|..|+
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d----TSAfV~l~~r~~~~~v~   59 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND----TSAFVALHNRDQAKVVM   59 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT----TEEEEEECCCHHHHHHH
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC----CcEEEEeecHHHHHHHH
Confidence            34556666 999999999999999999975 445544    47999999999999886

; 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.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.39  E-value=0.0019  Score=51.13  Aligned_cols=58  Identities=19%  Similarity=0.260  Sum_probs=46.0

Q ss_pred             HHHHHHh-hcCceeEEEeecCCC--CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          117 DLRRYFS-RFGRILDVYVPKRTG--HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       117 ~l~~~f~-~~G~v~~~~~~~~~~--~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      +|...|+ +||+|+++.|-.+-+  -.|-++|.|...++|++|+  +++-.+.|++|...+..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3444444 899999987764433  6788999999999999998  47789999999988764

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.35  E-value=0.035  Score=34.52  Aligned_cols=54  Identities=19%  Similarity=0.273  Sum_probs=43.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhc---CceeEEEeecCCCCcceEEEEEcChHHHHHHHhc
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRF---GRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR  159 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~---G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~  159 (234)
                      ..+|+|.++. +++.++|+.+|..|   .....|.++.+    .-|-|.|.+.+.|.+||..
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD----tScNvvf~d~~~A~~AL~~   61 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD----TSCNVVFKDEETAARALVA   61 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC----CcEEEEECCHHHHHHHHHc
Confidence            4689999995 57888999999998   12456777755    2588999999999999854

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.17  E-value=0.006  Score=50.43  Aligned_cols=37  Identities=19%  Similarity=0.453  Sum_probs=33.0

Q ss_pred             ccceEEEEEcCHHHHHHHHh---cCceeCCcEEEEeeccC
Q 026724           10 HRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATP   46 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~---~~~~i~gr~i~v~~a~~   46 (234)
                      .+++|||+|.+.+.|+.|.+   +...|+|+.|.|.|..+
T Consensus       263 ~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  263 RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            46799999999999999996   45589999999999987

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.15  E-value=0.0067  Score=53.53  Aligned_cols=76  Identities=11%  Similarity=0.148  Sum_probs=58.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHh-hcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcCC-----ccCCeEeEE
Q 026724           97 SQRIGKKIFVGRLPQEATAEDLRRYFS-RFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH-----EICGQQVAI  170 (234)
Q Consensus        97 ~~~~~~~l~v~nl~~~~~~~~l~~~f~-~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~-----~~~g~~i~v  170 (234)
                      ....++.|||.||-.-.|.-+|+.++. ..|.|++. +|..  .|..|||.|.+.++|.+....+|     .-+.+.|.+
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDk--IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDK--IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH-HHHH--hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            466788999999999999999999998 46666666 5421  36789999999999988653322     446678888


Q ss_pred             EeCCC
Q 026724          171 DSATP  175 (234)
Q Consensus       171 ~~a~~  175 (234)
                      .|+..
T Consensus       517 df~~~  521 (718)
T KOG2416|consen  517 DFVRA  521 (718)
T ss_pred             eecch
Confidence            88753

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=96.04  E-value=0.0074  Score=53.08  Aligned_cols=45  Identities=24%  Similarity=0.420  Sum_probs=38.0

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHhcCc--eeCCcEEEEeeccC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMVDTH--ELGGSTVVVDRATP   46 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~~~~--~i~gr~i~v~~a~~   46 (234)
                      +.+..|--.|.|+||++.+.++|.+||++.|  +|.|+.|.|..+..
T Consensus       438 VTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  438 VTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             eecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            3445566678999999999999999998766  89999999998754

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.92  E-value=0.0059  Score=51.79  Aligned_cols=74  Identities=19%  Similarity=0.394  Sum_probs=57.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCc--eeEEEeecCCCCcceEEEEEcChHHHHHHHh--cC-CccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RS-HEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~--v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~-~~~~g~~i~v~~a~~~  176 (234)
                      ++||++||.+.++..+|+.+|...-.  -..+ ++    ..+|+||...+...|.+|++  ++ .++.|.++.|....++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f-l~----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LV----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-ee----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            47999999999999999999965411  1111 22    35899999999999999985  33 3899999999998887


Q ss_pred             CCCC
Q 026724          177 DDAG  180 (234)
Q Consensus       177 ~~~~  180 (234)
                      ..+.
T Consensus        77 kqrs   80 (584)
T KOG2193|consen   77 KQRS   80 (584)
T ss_pred             HHHh
Confidence            6543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.89  E-value=0.06  Score=39.12  Aligned_cols=74  Identities=20%  Similarity=0.164  Sum_probs=54.2

Q ss_pred             CCCCCEEEEeCCCCCC-CHHH---HHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcCC-ccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEA-TAED---LRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH-EICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~-~~~~---l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~-~~~g~~i~v~~  172 (234)
                      .++..+|.|.=|..++ ..+|   +...++.||+|.+|.+.-    +--|.|.|.+..+|.+|+...+ ...|..+.+.|
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG----rqsavVvF~d~~SAC~Av~Af~s~~pgtm~qCsW  158 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG----RQSAVVVFKDITSACKAVSAFQSRAPGTMFQCSW  158 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC----CceEEEEehhhHHHHHHHHhhcCCCCCceEEeec
Confidence            4567788888776665 2334   445567899999998872    3469999999999999986433 66677788877


Q ss_pred             CCC
Q 026724          173 ATP  175 (234)
Q Consensus       173 a~~  175 (234)
                      -.+
T Consensus       159 qqr  161 (166)
T PF15023_consen  159 QQR  161 (166)
T ss_pred             ccc
Confidence            653

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=95.77  E-value=0.012  Score=53.52  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=37.0

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      -+||+|||++....+|.+||.  +.+.+..+.|+|.|+..+...
T Consensus       455 ~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  455 PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            579999999999999999994  578999999999999876543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.67  E-value=0.026  Score=48.61  Aligned_cols=72  Identities=19%  Similarity=0.235  Sum_probs=56.2

Q ss_pred             CEEEEeCCCCCC-CHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~-~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~~  176 (234)
                      +.|-+.-.|+.. +-++|...|.+||+|..|.|-..   --.|.|+|.+..+|-.|. .....|+++.|+|.|-.+.
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~---~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS---SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc---hhhheeeeeccccccchhccccceecCceeEEEEecCC
Confidence            444444455555 67899999999999999988622   246899999999996664 5778999999999998873

>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=94.66  E-value=0.069  Score=35.22  Aligned_cols=36  Identities=14%  Similarity=0.308  Sum_probs=26.4

Q ss_pred             ccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeecc
Q 026724           10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRAT   45 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~   45 (234)
                      +.+-|.|.|.+.+.|++|.  +++..+.|++|.|.+..
T Consensus        38 ~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   38 SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             -TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            5688999999999999999  47888999999998873

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

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.66  E-value=0.11  Score=45.88  Aligned_cols=69  Identities=10%  Similarity=0.233  Sum_probs=53.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhh--cCceeEEEee-cCCCCcceEEEEEcChHHHHHHH----hcCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSR--FGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVS----RRSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~--~G~v~~~~~~-~~~~~~g~afV~f~~~~~a~~A~----~~~~~~~g~~i~v  170 (234)
                      ...-|.|.|+-||..+-+++++.+|+.  |-.+.+|.+- .+     -=||+|++..||+.|.    +.-++|.|++|..
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-----nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-----NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-----ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            455677888999999999999999964  7788888876 32     2489999999999995    2455777776644


Q ss_pred             E
Q 026724          171 D  171 (234)
Q Consensus       171 ~  171 (234)
                      .
T Consensus       247 R  247 (684)
T KOG2591|consen  247 R  247 (684)
T ss_pred             h
Confidence            3

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=94.63  E-value=0.017  Score=48.52  Aligned_cols=55  Identities=16%  Similarity=0.120  Sum_probs=44.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCCCcceEEEEEcChHHHHHHHh
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      .+|+|.+|+..+...++.+.|..+|.|....+. ..  ..-+|-|+|....+...|+.
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~--~s~~c~~sf~~qts~~halr  207 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTASKS--RSSSCSHSFRKQTSSKHALR  207 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccC--CCcchhhhHhhhhhHHHHHH
Confidence            679999999999999999999999999877665 22  24566688887777777764

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.46  E-value=0.0097  Score=54.94  Aligned_cols=76  Identities=17%  Similarity=0.293  Sum_probs=57.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...+.+||++||+..+++.+|+..|..+|.|.+|.|- ..-+ --.|+||.|.+.+.+..|..  .+..|..-.+++.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            5567899999999999999999999999999999887 2222 34689999999988888753  333333334444444

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.87  E-value=0.45  Score=38.97  Aligned_cols=72  Identities=15%  Similarity=0.256  Sum_probs=51.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh-cCCccCCeE-eEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR-RSHEICGQQ-VAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~-i~v~~a~~~  176 (234)
                      ..-|-|-++|+...- .|..+|++||.|++.....   .-.|-+|.|.+.-+|++||. ++..|++.. |-|+-+..+
T Consensus       197 D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~~---ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTPS---NGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             cceEEEeccCccchh-HHHHHHHhhCeeeeeecCC---CCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCCH
Confidence            455666688776554 4667899999998765542   24688999999999999994 677777764 345554433

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=93.58  E-value=0.051  Score=45.29  Aligned_cols=47  Identities=15%  Similarity=0.280  Sum_probs=41.7

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      -+|+.|+++||-|-|+|++.-.|+.||.  +...+.+.+|+|-.|..+.
T Consensus       107 y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  107 YTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             cccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            4789999999999999999999999996  5788999999998887655

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.51  E-value=0.027  Score=46.56  Aligned_cols=77  Identities=23%  Similarity=0.329  Sum_probs=55.6

Q ss_pred             CCCEEEEeCCCCCCCHHH-H--HHHHhhcCceeEEEeecCC----C--CcceEEEEEcChHHHHHHHh--cCCccCCeEe
Q 026724          100 IGKKIFVGRLPQEATAED-L--RRYFSRFGRILDVYVPKRT----G--HRGFGFVTFAEEVVADRVSR--RSHEICGQQV  168 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~-l--~~~f~~~G~v~~~~~~~~~----~--~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i  168 (234)
                      ...-+||-+|+..+..++ |  .+.|.+||.|..|.+.+++    .  ...-++|+|...++|..||.  ++..++|+.|
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            446688889988775444 4  3688999999998877432    1  22337999999999999986  4557777777


Q ss_pred             EEEeCCCC
Q 026724          169 AIDSATPL  176 (234)
Q Consensus       169 ~v~~a~~~  176 (234)
                      +..+..++
T Consensus       156 ka~~gttk  163 (327)
T KOG2068|consen  156 KASLGTTK  163 (327)
T ss_pred             HHhhCCCc
Confidence            77666554

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=92.96  E-value=0.11  Score=45.88  Aligned_cols=42  Identities=21%  Similarity=0.351  Sum_probs=31.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeC-CcEEEEee
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELG-GSTVVVDR   43 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~-gr~i~v~~   43 (234)
                      +|-|..+| ++||.|++|++..+|+.|++  +++.|+ .++..|..
T Consensus        96 ~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen   96 YPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             eccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence            35577755 99999999999999999995  566554 45555543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.29  E-value=4.6  Score=37.36  Aligned_cols=69  Identities=6%  Similarity=0.035  Sum_probs=44.3

Q ss_pred             CEEEEe-CCCCCCCHHHHHHHHhhcCcee-----EEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724          102 KKIFVG-RLPQEATAEDLRRYFSRFGRIL-----DVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus       102 ~~l~v~-nl~~~~~~~~l~~~f~~~G~v~-----~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      .++||. +=-..++..+|..++..-+.|.     .|.|.     ..|.||+..... |...+  ++...+.|+.|.|+.+
T Consensus       487 ~~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~-----~~~s~v~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  560 (629)
T PRK11634        487 QLYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLF-----ASHSTIELPKGM-PGEVLQHFTRTRILNKPMNMQLL  560 (629)
T ss_pred             EEEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEe-----CCceEEEcChhh-HHHHHHHhccccccCCceEEEEC
Confidence            446653 2245678888888887665543     34553     358899876433 44444  3556899999999987


Q ss_pred             CCC
Q 026724          174 TPL  176 (234)
Q Consensus       174 ~~~  176 (234)
                      ...
T Consensus       561 ~~~  563 (629)
T PRK11634        561 GDA  563 (629)
T ss_pred             CCC
Confidence            533

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=92.09  E-value=0.07  Score=44.01  Aligned_cols=50  Identities=20%  Similarity=0.540  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ++.++.|+.++|||||.|.+..++..+++ ..+.+.++++.+....+....
T Consensus       217 ~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  217 LPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             cCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCCCccc
Confidence            45678899999999999999999999998 567899999999988766443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=91.55  E-value=0.21  Score=43.33  Aligned_cols=39  Identities=28%  Similarity=0.557  Sum_probs=32.7

Q ss_pred             CCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccC
Q 026724            8 KAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATP   46 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~   46 (234)
                      +++..||||+|++.++++.||+ +...|++++|.|+.-.+
T Consensus       327 ~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  327 GKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             CCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccc
Confidence            4444999999999999999996 57789999999986543

>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=91.33  E-value=0.94  Score=34.85  Aligned_cols=61  Identities=16%  Similarity=0.184  Sum_probs=41.8

Q ss_pred             CHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--c--CCccCCeEeEEEeCCCCC
Q 026724          114 TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--R--SHEICGQQVAIDSATPLD  177 (234)
Q Consensus       114 ~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~--~~~~~g~~i~v~~a~~~~  177 (234)
                      ..+.|+++|..++.+..+.+.+.   -+-..|.|.+.++|..|..  +  ...+.|..++|-++.+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s---FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS---FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT---TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC---CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            45789999999999888776643   3457899999999999964  4  568999999999985443

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.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=91.31  E-value=0.33  Score=42.85  Aligned_cols=142  Identities=19%  Similarity=0.193  Sum_probs=77.9

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAP   81 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (234)
                      ++.|-..+|..||+|-|..+|+.|++  +..+|.|+.|..    +........-   +.+          ..-......+
T Consensus       105 ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~----~~~~~~~~~~---~~~----------~~~~~~~~~p  167 (549)
T KOG4660|consen  105 IRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKR----PGGARRAMGL---QSG----------TSFLNHFGSP  167 (549)
T ss_pred             hhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcC----CCcccccchh---ccc----------chhhhhccch
Confidence            35677889999999999999999995  677888888861    1111111000   000          0000011111


Q ss_pred             CccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhc-C
Q 026724           82 TLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR-S  160 (234)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-~  160 (234)
                      .....+..         -.-..+|+ .|++..+...++..|+-+|.+.. +....  ..---|++|.+..++..++.. +
T Consensus       168 ~a~s~pgg---------~~~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~~~~--~~hq~~~~~~~~~s~a~~~~~~G  234 (549)
T KOG4660|consen  168 LANSPPGG---------WPRGQLFG-MLSPTRSSILLEHISSVDGSSPG-RETPL--LNHQRFVEFADNRSYAFSEPRGG  234 (549)
T ss_pred             hhcCCCCC---------CcCCccee-eeccchhhhhhhcchhccCcccc-ccccc--hhhhhhhhhccccchhhcccCCc
Confidence            11111111         01223333 38888888777778888888765 33210  122457888888887555532 4


Q ss_pred             CccCCeEeEEEeCCC
Q 026724          161 HEICGQQVAIDSATP  175 (234)
Q Consensus       161 ~~~~g~~i~v~~a~~  175 (234)
                      ..+.+....+.++.+
T Consensus       235 ~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  235 FLISNSSGVITFSGP  249 (549)
T ss_pred             eecCCCCceEEecCC
Confidence            455555555555544

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=91.22  E-value=0.17  Score=45.51  Aligned_cols=69  Identities=20%  Similarity=0.258  Sum_probs=56.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..+..++||+|+...+..+-++.+...+|.|.++...      -|+|++|..+.....|+.  ....+++..+.+..
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh------hhcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            4567799999999999999999999999999877553      399999999998888863  45577777766654

>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=90.42  E-value=0.35  Score=36.93  Aligned_cols=75  Identities=16%  Similarity=0.175  Sum_probs=42.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhh-cCce---eEEE--ee-cCCC--CcceEEEEEcChHHHHHHHh--cCCccCC---
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSR-FGRI---LDVY--VP-KRTG--HRGFGFVTFAEEVVADRVSR--RSHEICG---  165 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~-~G~v---~~~~--~~-~~~~--~~g~afV~f~~~~~a~~A~~--~~~~~~g---  165 (234)
                      ...+|.|++||+++||+++.+.++. ++..   ..+.  +. ....  .-.-|||.|.+.+++..-..  +++.+.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4569999999999999999887766 5544   3333  11 1111  33568999999998666543  4442221   


Q ss_pred             --eEeEEEeCC
Q 026724          166 --QQVAIDSAT  174 (234)
Q Consensus       166 --~~i~v~~a~  174 (234)
                        ....|++|.
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence              345666664

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.

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=90.39  E-value=0.54  Score=44.41  Aligned_cols=17  Identities=18%  Similarity=0.122  Sum_probs=9.4

Q ss_pred             CCCccceEEEEEcCHHH
Q 026724            7 SKAHRGIGFITFASADS   23 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~   23 (234)
                      .|+-++|+--.|++.-.
T Consensus       898 ~g~q~~~~g~kfsdhva  914 (1282)
T KOG0921|consen  898 SGTQRKFAGNKFSDHVA  914 (1282)
T ss_pred             ccchhhccccccccchh
Confidence            45556666666655433

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=89.43  E-value=0.8  Score=36.77  Aligned_cols=44  Identities=14%  Similarity=0.248  Sum_probs=37.8

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      +|+|.|.|=|.|...+||++||+  ++..|+|+++.+....+....
T Consensus       120 ~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~~~  165 (243)
T KOG0533|consen  120 AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPSQS  165 (243)
T ss_pred             CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcccc
Confidence            58999999999999999999995  678999999999887655443

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=89.36  E-value=0.24  Score=36.62  Aligned_cols=84  Identities=15%  Similarity=0.188  Sum_probs=58.2

Q ss_pred             CccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccCCC
Q 026724            9 AHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (234)
                      ...++..++|.+.+++++++.. ...+.+..+.++.-.+........                                 
T Consensus        53 l~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~~~---------------------------------   99 (153)
T PF14111_consen   53 LGDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDFNPSEVK---------------------------------   99 (153)
T ss_pred             eCCCeEEEEEEeccceeEEEecccccccccchhhhhhcccccccccc---------------------------------
Confidence            3568899999999999999964 457778777776655432211000                                 


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEee
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVP  134 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~  134 (234)
                               ......-|-|.|||.. .+++-|+.+-+.+|.+..+...
T Consensus       100 ---------~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen  100 ---------FEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             ---------eeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence                     0112233556799988 4888899999999999888765

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=88.50  E-value=0.78  Score=33.69  Aligned_cols=34  Identities=24%  Similarity=0.399  Sum_probs=28.3

Q ss_pred             eEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccC
Q 026724           13 IGFITFASADSVENLM-VDTHELGGSTVVVDRATP   46 (234)
Q Consensus        13 ~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~   46 (234)
                      -=+|+|.+-+.|-+|+ +++..+.|+.|.|+.-.+
T Consensus        72 ~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   72 TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE---
T ss_pred             eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCc
Confidence            4589999999999999 589999999999987654

; PDB: 1UFW_A 2DNR_A.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=87.11  E-value=0.4  Score=38.33  Aligned_cols=37  Identities=14%  Similarity=0.252  Sum_probs=32.2

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      .-+|=++|.|..+|+|++|++  |+..+.|++|...+..
T Consensus       108 hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen  108 HLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             hhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            456789999999999999994  7889999999988764

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=85.85  E-value=1.7  Score=35.36  Aligned_cols=34  Identities=29%  Similarity=0.615  Sum_probs=27.0

Q ss_pred             CCEEEEeCCCCC------------CCHHHHHHHHhhcCceeEEEee
Q 026724          101 GKKIFVGRLPQE------------ATAEDLRRYFSRFGRILDVYVP  134 (234)
Q Consensus       101 ~~~l~v~nl~~~------------~~~~~l~~~f~~~G~v~~~~~~  134 (234)
                      ..+||+.+||-.            .+++-|+..|+.||.|..|.|+
T Consensus       149 pdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdip  194 (445)
T KOG2891|consen  149 PDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIP  194 (445)
T ss_pred             CCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCc
Confidence            456777777632            3678899999999999998887

>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=85.57  E-value=10  Score=26.55  Aligned_cols=63  Identities=13%  Similarity=0.152  Sum_probs=43.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCc-eeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCcc
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEI  163 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~  163 (234)
                      ...+.+...|+.++-++|..+.+.+-. |..++|+++.. ++=.+.+.|.+.++|..-..  |+..+
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            344445556666677778766666654 56678876655 77789999999999888653  55533

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=85.38  E-value=0.6  Score=43.48  Aligned_cols=76  Identities=16%  Similarity=0.200  Sum_probs=58.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCC--ccCCeEeEEEeCCCCCC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSH--EICGQQVAIDSATPLDD  178 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~--~~~g~~i~v~~a~~~~~  178 (234)
                      +.++-|.+-+.+-..|..+|++||.|.+++..++   -..|.|+|.+.+.|..|+.  .+.  .+.|-+.+|.+|+.-+-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~---~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~  376 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD---LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPM  376 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc---ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccccc
Confidence            3455556667788899999999999999988754   3679999999999999873  333  55678899999987664


Q ss_pred             CCC
Q 026724          179 AGP  181 (234)
Q Consensus       179 ~~~  181 (234)
                      -.+
T Consensus       377 ~ep  379 (1007)
T KOG4574|consen  377 YEP  379 (1007)
T ss_pred             ccC
Confidence            443

>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=82.88  E-value=10  Score=24.30  Aligned_cols=65  Identities=25%  Similarity=0.376  Sum_probs=34.0

Q ss_pred             EEEEe-CCCCCCCHHHHHHHHhhcCc-----eeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724          103 KIFVG-RLPQEATAEDLRRYFSRFGR-----ILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus       103 ~l~v~-nl~~~~~~~~l~~~f~~~G~-----v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      +|||. +--..++..+|..++...+.     |-.|.|..     .|+||+-... .|..++  ++...+.|++|.|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-----~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD-----NFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S-----S-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee-----eEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45552 22346788899888876644     45566643     5899988754 455555  4667999999999865

; PDB: 2G0C_A 3MOJ_B.

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=82.26  E-value=1.5  Score=30.98  Aligned_cols=48  Identities=23%  Similarity=0.418  Sum_probs=26.1

Q ss_pred             EEEEeCCCCC---------CCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcCh
Q 026724          103 KIFVGRLPQE---------ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE  150 (234)
Q Consensus       103 ~l~v~nl~~~---------~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~  150 (234)
                      .+.|-|++..         .+.+.|++.|+.|..++...+....++.++++|+|.+.
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~kv~~l~~~~gh~g~aiv~F~~~   66 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLKVKPLYGKQGHTGFAIVEFNKD   66 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---SEEEEEEETTEEEEEEEEE--SS
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCceeEECcCCCCCcEEEEEEECCC
Confidence            4566677543         35578999999998876443434445889999999864

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>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=81.01  E-value=3.7  Score=28.24  Aligned_cols=36  Identities=19%  Similarity=0.149  Sum_probs=27.6

Q ss_pred             ccceEEEEEcCHHHHHHHH-hcCceeCCcE-EEEeecc
Q 026724           10 HRGIGFITFASADSVENLM-VDTHELGGST-VVVDRAT   45 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al-~~~~~i~gr~-i~v~~a~   45 (234)
                      ....-.|+|.++.+|.+|| +|+..|.|.. +-|.+..
T Consensus        53 ~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   53 GGNWIHITYDNPLSAQRALQKNGTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             CTTEEEEEESSHHHHHHHHTTTTEEETTCEEEEEEE-H
T ss_pred             CCCEEEEECCCHHHHHHHHHhCCeEEcCcEEEEEEEcH
Confidence            3457889999999999999 5888998864 4466553

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	234
3d2w_A	89	Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Co		1e-10
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-09
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		3e-09
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		5e-08
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		1e-07
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		1e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		4e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		3e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-07
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		7e-07
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		7e-07
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		9e-07
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		3e-06
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		3e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		6e-06
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		1e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-05
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		3e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		5e-05
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		1e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		1e-04
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		4e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-04
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		6e-04

>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex Wit Length = 89

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 48/75 (64%), Gaps = 2/75 (2%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRS 160
           G K+FVGR  ++ TAE+L+++F ++G ++DV++PK    R F FVTFA++ VA  +    
Sbjct: 11  GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK--PFRAFAFVTFADDKVAQSLCGED 68
Query: 161 HEICGQQVAIDSATP 175
             I G  V I +A P
Sbjct: 69  LIIKGISVHISNAEP 83

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 50/86 (58%), Gaps = 6/86 (6%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV---YVPKRTGHRGFGFVTFAEEVVADR-VSR 158
           KIFVG +P      +LR YF +FG + +V   Y  ++   RGFGF+TF +E   D+ V+ 
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 159 RSHEICGQQVAIDSATPLD--DAGPS 182
             H+I G++V +  A P D   +GPS
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSSGPS 97

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 4/81 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEI 163
           +FVGR   + T ++LR +FS++G ++DV++PK    R F FVTFA++ +A  +      I
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCGEDLII 65
Query: 164 CGQQVAIDSATPL--DDAGPS 182
            G  V I +A P    ++GPS
Sbjct: 66  KGISVHISNAEPKHNSNSGPS 86

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 54.3 bits (129), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 50/90 (55%), Gaps = 6/90 (6%)
Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVAD 154
           Q+    I +G LP + T +DL+ YFS FG +L V V K  +TGH +GFGFV F E     
Sbjct: 13  QKTSDLIVLG-LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Query: 155 RVSRRSHEICGQ--QVAIDSATPLDDAGPS 182
           +V  + H I G+     + ++    D+GPS
Sbjct: 72  KVMSQRHMIDGRWCDCKLPNSKQSQDSGPS 101

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 50/86 (58%), Gaps = 5/86 (5%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVSRRS 160
           K++ V  +P      DLR+ F +FG+ILDV +     G +GFGFVTF     ADR   + 
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 161 H--EICGQQVAIDSATP--LDDAGPS 182
           H   + G+++ +++AT   + ++GPS
Sbjct: 76  HGTVVEGRKIEVNNATARVMTNSGPS 101

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTG-HRGFGFVTFAEEVVADRVSR-R 159
           IFVG L    T ED++ YF +FG++ D  +   K T  HRGFGFVTF  E + ++V    
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 160 SHEICGQQVAIDSA 173
            HEI  + V    A
Sbjct: 62  FHEINNKMVECKKA 75

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 48  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 99
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 100 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 125
Query: 122 FSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
           F ++G+I  +++   + +G  RGF FVTF +    D+ V ++ H + G    +  A
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 181

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 11/132 (8%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT+A  EEV A  +
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 73
Query: 157 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 211
           + R H++ G+ V    A   +D+      +       GG         +R Y   YG ++
Sbjct: 74  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 133
Query: 212 FDDWGYGMGSGR 223
             +     GSG+
Sbjct: 134 VIEIMTDRGSGK 145

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 45/86 (52%), Gaps = 6/86 (6%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTGHRGFGFVTFAE-EVVADRVSR 158
           K+FVG L    T E LR YFS++G ++D  + K       RGFGFV F +   V   ++ 
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 159 RSHEICGQQVAIDSATP--LDDAGPS 182
           R H + G+ +     TP  +  +GPS
Sbjct: 78  RPHTLDGRNIDPKPCTPRGMQPSGPS 103

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 47  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 98
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 99  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 124
Query: 122 FSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
           F ++G+I  +++   + +G  RGF FVTF +    D+ V ++ H + G    +  A
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 180

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 11/132 (8%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT+A  EEV A  +
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 72
Query: 157 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 211
           + R H++ G+ V    A   +D+      +       GG         +R Y   YG ++
Sbjct: 73  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 212 FDDWGYGMGSGR 223
             +     GSG+
Sbjct: 133 VIEIMTDRGSGK 144

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 46  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 97
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 98  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 123
Query: 122 FSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
           F ++G+I  +++   + +G  RGF FVTF +    D+ V ++ H + G    +  A
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 179

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 11/132 (8%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT+A  EEV A  +
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 71
Query: 157 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 211
           + R H++ G+ V    A   +D+      +       GG         +R Y   YG ++
Sbjct: 72  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 131
Query: 212 FDDWGYGMGSGR 223
             +     GSG+
Sbjct: 132 VIEIMTDRGSGK 143

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 47  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 98
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 99  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 124
Query: 122 FSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
           F ++G+I  +++   + +G  RGF FVTF +    D+ V ++ H + G    +  A
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 180

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 11/132 (8%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT+A  EEV A  +
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 72
Query: 157 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 211
           + R H++ G+ V    A   +D+      +       GG         +R Y   YG ++
Sbjct: 73  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 212 FDDWGYGMGSGR 223
             +     GSG+
Sbjct: 133 VIEIMTDRGSGK 144

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 45  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 96
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 97  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 122
Query: 122 FSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
           F ++G+I  +++   + +G  RGF FVTF +    D+ V ++ H + G    +  A
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 178

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 11/132 (8%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT+A  EEV A  +
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 70
Query: 157 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 211
           + R H++ G+ V    A   +D+      +       GG         +R Y   YG ++
Sbjct: 71  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 130
Query: 212 FDDWGYGMGSGR 223
             +     GSG+
Sbjct: 131 VIEIMTDRGSGK 142

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 40  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 91
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 92  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 117
Query: 122 FSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
           F ++G+I  +++   + +G  RGF FVTF +    D+ V ++ H + G    +  A
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 173

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 11/132 (8%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA--EEVVADRV 156
           +K+F+G L  E T E LR +F ++G + D  V   P     RGFGFVT+A  EEV A  +
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 65
Query: 157 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 211
           + R H++ G+ V    A   +D+      +       GG         +R Y   YG ++
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125
Query: 212 FDDWGYGMGSGR 223
             +     GSG+
Sbjct: 126 VIEIMTDRGSGK 137

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 50.8 bits (120), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 3/76 (3%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGHRGFGFVTFAEEVVADRVSRRS 160
           K++ V  +P      DLR+ F +FG+ILDV +     G +GFGFVTF     ADR   + 
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 161 H--EICGQQVAIDSAT 174
           H   + G+++ +++AT
Sbjct: 90  HGTVVEGRKIEVNNAT 105

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 45/87 (51%), Gaps = 4/87 (4%)
Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAE 149
           RG      G K+F+G L  + T E LR YF +FG + +  V   P     RGFGFVTF +
Sbjct: 17  RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
Query: 150 EVVADRVSRRS-HEICGQQVAIDSATP 175
           +   D+V  +S HE+  + +    A P
Sbjct: 77  QAGVDKVLAQSRHELDSKTIDPKVAFP 103

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 45/83 (54%), Gaps = 4/83 (4%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVAD-RVS 157
           +K+F+G L  E T E LR Y+ ++G++ D  V   P     RGFGFVTF+     D  ++
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 158 RRSHEICGQQVAIDSATPLDDAG 180
            R H I G+ V    A   +++G
Sbjct: 88  ARPHSIDGRVVEPKRAVAREESG 110

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGH-RGFGFVTFAEEVVADRVSRR 159
           K+F+G L  + T ++LR YF ++G + D+ + K   TG  RGFGF++F +    D V + 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 160 SHEICGQQVAIDSATPLDD 178
            H + G+ +    A P D+
Sbjct: 65  QHILDGKVIDPKRAIPRDE 83

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVSRR 159
           K+F+G L  + T E LR YF +FG + +  V   P     RGFGFVTF ++   D+V  +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 160 S-HEI 163
           S HE+
Sbjct: 62  SRHEL 66

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SRR 159
           +F+G L  + T +DL+ YFS+FG ++D  +   P     RGFGFV F E    D+V  ++
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 160 SHEICGQQV 168
            H++ G+ +
Sbjct: 62  EHKLNGKVI 70

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFAEEVVADRVSRR 159
           KIFVG LP   T   LR+YF  FG I +  V   ++TG  RG+GFVT A+   A+R  + 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 160 SHEI 163
            + I
Sbjct: 79  PNPI 82

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 9/84 (10%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH- 161
           K+F+G LP+EAT +++R  F ++G++L+  + K      +GFV   ++  A+   R  H 
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-----YGFVHIEDKTAAEDAIRNLHH 64
Query: 162 -EICGQQVAIDSATPLDDA--GPS 182
            ++ G  + ++++     A  GPS
Sbjct: 65  YKLHGVNINVEASKNKSKASSGPS 88

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 4/78 (5%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV---YVPKRTGHRGFGFVTFAEEVVADRVSR 158
           + I+VG L   AT+E ++  FS+FG++ +V   Y  +    +GFGFV   EE V++ +++
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 159 RSH-EICGQQVAIDSATP 175
             + +  G+ + +  A P
Sbjct: 62  LDNTDFMGRTIRVTEANP 79

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 4/70 (5%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-SR 158
           K FVG L  + + +DL+ YF++FG ++D  +   P     RGFGF+ F +    ++V  +
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 159 RSHEICGQQV 168
           + H + G+ +
Sbjct: 73  KEHRLDGRVI 82

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRV-S 157
           KKIFVG L  +   E +R YF  FG +  + +P   K    RGF F+TF EE    ++  
Sbjct: 2   KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 158 RRSHEI----CGQQVAI 170
           ++ H +    C  +VA+
Sbjct: 62  KKYHNVGLSKCEIKVAM 78

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFA 148
           SF   GE +     ++FVG LP + T ED +R F R+G   +V++ +    RGFGF+   
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR---DRGFGFIRLE 66
Query: 149 EEVVAD 154
              +A+
Sbjct: 67  SRTLAE 72

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 7/86 (8%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADR--VSR 158
           +FVG L  E T ED++  F+ FG+I D  V K   TG  +G+GFV+F  ++ A+   V  
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 159 RSHEICGQQVAIDSAT--PLDDAGPS 182
               + G+Q+  + AT  P   +GPS
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPSGPS 103

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRT----GHRGFGFVTF 147
           KI V  +P +A   ++R  FS FG +  V +PK+      HRGFGFV F
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRRS 160
           IFVG L  +   E +R YF  FG +  + +P   K    RGF F+TF EE    ++  + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 161 HEICG 165
           +   G
Sbjct: 62  YHNVG 66

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TG-HRGFGFVTFAEEVVADRVSRR 159
           K+F+G++P+    +DL+  F  FG+I ++ V K   TG H+G  F+T+ E   A +    
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 160 SHE 162
            HE
Sbjct: 75  LHE 77

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/89 (34%), Positives = 47/89 (52%), Gaps = 11/89 (12%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTGHRGFGFVTFAEEVVAD----R 155
           K+FVG L  +   + L + FS++G+I +V V K       RGFGFVTF  E + D     
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF--ENIDDAKDAM 71
Query: 156 VSRRSHEICGQQVAIDSATPLDD--AGPS 182
           ++     + G+Q+ +D A    D  +GPS
Sbjct: 72  MAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVSRR- 159
           +FVG L  E T ED++  F+ FGRI D  V K   TG  +G+GFV+F  +  A+   ++ 
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 160 -SHEICGQQVAIDSAT 174
               + G+Q+  + AT
Sbjct: 78  GGQWLGGRQIRTNWAT 93

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSRR 159
           K+FVG++P+    +DL+  F  FGRI ++ V K   TG H+G  F+T+     A +    
Sbjct: 17  KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 160 SHE 162
            HE
Sbjct: 77  LHE 79

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 47/84 (55%), Gaps = 5/84 (5%)
Query: 89  SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFA 148
           +F   GE +     ++FVG LP + T E++R+ F ++G+  +V++ K    +GFGF+   
Sbjct: 10  NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLE 66
Query: 149 EEVVAD--RVSRRSHEICGQQVAI 170
              +A+  +V   +  + G+Q+ +
Sbjct: 67  TRTLAEIAKVELDNMPLRGKQLRV 90

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD--RVSRRS 160
           ++FVG LP + T E++R+ F ++G+  +V++ K    +GFGF+      +A+  +V   +
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDN 73
Query: 161 HEICGQQVAIDSAT 174
             + G+Q+ +  A 
Sbjct: 74  MPLRGKQLRVRFAC 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	234
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-37
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-22
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-33
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	7e-32
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-31
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-26
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-25
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-24
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-21
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-21
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-21
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-21
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-20
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-20
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-19
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	9e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-19
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-19
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-06
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-05
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-18
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	7e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-04
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-14
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	9e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-13
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-13
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-12
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-12
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	9e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-11
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-11
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	7e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-10
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-10
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-10
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	9e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-09
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-04
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-09
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	8e-04
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	9e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-08
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-07
2div_A	99	TRNA selenocysteine associated protein; structural	9e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-06
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-04

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  127 bits (321), Expect = 3e-37
 Identities = 41/179 (22%), Positives = 68/179 (37%), Gaps = 52/179 (29%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           + KD  +   RG GF++F    SV+ ++   H L G  +   RA P+++  +        
Sbjct: 35  IMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKT------- 87

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
                                                     KIFVG +  +   ++   
Sbjct: 88  -----------------------------------------GKIFVGGIGPDVRPKEFEE 106

Query: 121 YFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV-SRRSHEICGQQVAIDSATP 175
           +FS++G I+D  +   K TG  RGFGFVT+      DRV   +  +   +++ I  A P
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP 165

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 87.2 bits (217), Expect = 9e-22
 Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 3/86 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSR 158
            K+F+G L  + T ++LR YF ++G + D+ + K   TG  RGFGF++F +    D V +
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 159 RSHEICGQQVAIDSATPLDDAGPSQN 184
             H + G+ +    A P D+   +  
Sbjct: 64  TQHILDGKVIDPKRAIPRDEQDKTGK 89

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 57.5 bits (140), Expect = 1e-10
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK 47
           +  D+ +   RG GF+T+ SAD+V+ +      +     + + RA P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  118 bits (299), Expect = 1e-33
 Identities = 43/187 (22%), Positives = 75/187 (40%), Gaps = 47/187 (25%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP   ++   
Sbjct: 47  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--- 103

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG + ++     LR Y
Sbjct: 104 ---------------------------------------VKKIFVGGIKEDTEEHHLRDY 124

Query: 122 FSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV-SRRSHEICGQQVAIDSATPLD 177
           F ++G+I  + +   + +G  RGF FVTF +    D++  ++ H + G    +  A    
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184

Query: 178 DAGPSQN 184
           +   + +
Sbjct: 185 EMASASS 191

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 85.0 bits (211), Expect = 1e-20
 Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRV-S 157
           +K+F+G L  E T E LR +F ++G + D  V     T   RGFGFVT+A     D   +
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73

Query: 158 RRSHEICGQQVAIDSATPLDDAGPSQ 183
            R H++ G+ V    A   +D+    
Sbjct: 74  ARPHKVDGRVVEPKRAVSREDSQRPG 99

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGR 56
           +  D+GS   RG  F+TF   DSV+ +++   H + G    V +A  K++       
Sbjct: 136 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS 192

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score =  110 bits (278), Expect = 7e-32
 Identities = 31/85 (36%), Positives = 49/85 (57%), Gaps = 2/85 (2%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
                  G K+FVGR  ++ TAE+L+++F ++G ++DV++PK    R F FVTFA++ VA
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP--FRAFAFVTFADDKVA 61

Query: 154 DRVSRRSHEICGQQVAIDSATPLDD 178
             +      I G  V I +A P  +
Sbjct: 62  QSLCGEDLIIKGISVHISNAEPKHN 86

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 55.7 bits (135), Expect = 9e-11
 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDF 51
          +PK       R   F+TFA     ++L  +   + G +V +  A PK +  
Sbjct: 43 IPKP-----FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHNKL 88

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score =  108 bits (273), Expect = 4e-31
 Identities = 28/87 (32%), Positives = 47/87 (54%), Gaps = 2/87 (2%)

Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS 157
                 +FVGR   + T ++LR +FS++G ++DV++PK    R F FVTFA++ +A  + 
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLC 59

Query: 158 RRSHEICGQQVAIDSATPLDDAGPSQN 184
                I G  V I +A P  ++    +
Sbjct: 60  GEDLIIKGISVHISNAEPKHNSNSGPS 86

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 12/46 (26%), Positives = 20/46 (43%)

Query: 8  KAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRP 53
          K  R   F+TFA     ++L  +   + G +V +  A PK +    
Sbjct: 39 KPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNSG 84

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 96.5 bits (241), Expect = 4e-26
 Identities = 32/94 (34%), Positives = 46/94 (48%), Gaps = 4/94 (4%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFA 148
           G   SS     KIFVG +P      +LR YF +FG + +V +         RGFGF+TF 
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 149 EEVVADRV-SRRSHEICGQQVAIDSATPLDDAGP 181
           +E   D+  +   H+I G++V +  A P D    
Sbjct: 61  DEQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSS 94

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
          M  D   +  RG GFITF    SV+  + +  H++ G  V V RA P++ 
Sbjct: 42 MIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDS 91

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 94.2 bits (235), Expect = 3e-25
 Identities = 32/99 (32%), Positives = 48/99 (48%), Gaps = 4/99 (4%)

Query: 84  YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HR 140
           + H      RG      G K+F+G L  + T E LR YF +FG + +  V +   T   R
Sbjct: 8   HHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR 67

Query: 141 GFGFVTFAEEVVADRV-SRRSHEICGQQVAIDSATPLDD 178
           GFGFVTF ++   D+V ++  HE+  + +    A P   
Sbjct: 68  GFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA 106

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 51.9 bits (125), Expect = 4e-09
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
           +D  +K  RG GF+TF     V+ ++    HEL   T+    A P+  
Sbjct: 59  RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA 106

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 91.4 bits (228), Expect = 2e-24
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV-SR 158
           KIFVG L  +   E +R YF  FG +  + +P   +T   RGF F+TF EE    ++  +
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 159 RSHEICGQQVAIDSA 173
           + H +   +  I  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 50.2 bits (121), Expect = 8e-09
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRA 44
          +P D  +   RG  FITF   + V+ +M    H +G S   +  A
Sbjct: 31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA 75

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

 Score = 83.7 bits (208), Expect = 2e-21
 Identities = 32/75 (42%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV-SR 158
           KIFVG L    T ED++ YF +FG++ D  +   K T  HRGFGFVTF  E + ++V   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 159 RSHEICGQQVAIDSA 173
             HEI  + V    A
Sbjct: 61  HFHEINNKMVECKKA 75

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

 Score = 46.3 bits (111), Expect = 2e-07
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRA 44
          +  D+ +  HRG GF+TF S D VE +     HE+    V   +A
Sbjct: 31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA 75

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 84.6 bits (210), Expect = 2e-21
 Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVSR 158
             + V  LP + T +DL+ YFS FG +L V V K  +TGH +GFGFV F E     +V  
Sbjct: 16  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

Query: 159 RSHEICGQQVAIDSATP 175
           + H I G+         
Sbjct: 76  QRHMIDGRWCDCKLPNS 92

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 10/47 (21%), Positives = 18/47 (38%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED 49
          KD  +   +G GF+ F   ++   +M   H + G          K+ 
Sbjct: 49 KDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS 95

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 84.2 bits (209), Expect = 2e-21
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTFAEEVVADRVSRR 159
             +FVG +       ++R +F+R+G + +V +   RTG  +G+GFV+F  +V   ++   
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69

Query: 160 SHEICGQQVAIDSATP 175
                G+++ +  A  
Sbjct: 70  QINFHGKKLKLGPAIR 85

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 8/39 (20%), Positives = 19/39 (48%)

Query: 11 RGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED 49
          +G GF++F +   V+ ++       G  + +  A  K++
Sbjct: 50 KGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRKQN 88

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

 Score = 86.2 bits (214), Expect = 6e-21
 Identities = 29/182 (15%), Positives = 64/182 (35%), Gaps = 44/182 (24%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           M  D  +  H+G  F+ +   ++ +  +  +++  LGG  + V R +             
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA-------- 111

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                             +     R   +I+V  + Q+ + +D+
Sbjct: 112 -----------------------------QPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142

Query: 119 RRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRV--SRRSHEICGQQVAIDSA 173
           +  F  FG+I    + +   TG H+G+GF+ + +   +     S    ++ GQ + +  A
Sbjct: 143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

Query: 174 TP 175
             
Sbjct: 203 VT 204

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

 Score = 69.6 bits (171), Expect = 8e-15
 Identities = 28/116 (24%), Positives = 51/116 (43%), Gaps = 10/116 (8%)

Query: 88  GSFYGRGESSQRIGK-----KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-H 139
           G   GRG ++QR G      +++VG +  E   + +R+ F+ FG I  + +     T  H
Sbjct: 10  GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKH 69

Query: 140 RGFGFVTFAEEVVADRVSRR--SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETF 193
           +GF FV +     A     +  S  + G+ + +   + +  A P  + +   A  F
Sbjct: 70  KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125

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

 Score = 41.5 bits (98), Expect = 8e-05
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
           + +D  +  H+G GFI +  A S ++ +  ++  +LGG  + V +A   
Sbjct: 157 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

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

 Score = 82.4 bits (204), Expect = 1e-20
 Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           G S     + +FV   P+   +  L  YF  FG +  V + K  G   F  V   +    
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG--VFAIVEMGDVGAR 58

Query: 154 DRV-SRRSHEICGQQVAIDSATPLDDAGPSQN 184
           + V S+  H + G ++ +      +   P+  
Sbjct: 59  EAVLSQSQHSLGGHRLRVRPREQKEFQSPASK 90

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

 Score = 39.6 bits (93), Expect = 8e-05
 Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 7/61 (11%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFRPVGRMSH 59
          M KD+G         +      + E  L    H LGG  + V     KE    P  +   
Sbjct: 40 MDKDKG-----VFAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEFQ-SPASKSPK 93

Query: 60 G 60
          G
Sbjct: 94 G 94

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

 Score = 82.3 bits (204), Expect = 2e-20
 Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 4/84 (4%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRV-S 157
           +K+F+G L  E T E LR Y+ ++G++ D  V +   +   RGFGFVTF+     D   +
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87

Query: 158 RRSHEICGQQVAIDSATPLDDAGP 181
            R H I G+ V    A   +++G 
Sbjct: 88  ARPHSIDGRVVEPKRAVAREESGS 111

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

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRP 53
           +D  SK  RG GF+TF+S   V+  M    H + G  V   RA  +E+    
Sbjct: 61  RDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSG 112

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 79.6 bits (197), Expect = 1e-19
 Identities = 34/98 (34%), Positives = 46/98 (46%), Gaps = 6/98 (6%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFA 148
           G   S      K+FVG L    T E LR YFS++G ++D  + K   T   RGFGFV F 
Sbjct: 7   GMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66

Query: 149 EEVVADRV-SRRSHEICGQQVAIDSATPLDD--AGPSQ 183
           +      V + R H + G+ +     TP     +GPS 
Sbjct: 67  DPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSGPSS 104

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 48.0 bits (115), Expect = 9e-08
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKED 49
          KD+ +   RG GF+ F   + V  ++    H L G  +     TP+  
Sbjct: 50 KDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGM 97

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

 Score = 78.7 bits (195), Expect = 2e-19
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRV-SR 158
           K+F+G L  + T E LR YF +FG + +  V +   T   RGFGFVTF ++   D+V ++
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 159 RSHEICGQQVAIDSA 173
             HE+  + +    A
Sbjct: 62  SRHELDSKTIDPKVA 76

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

 Score = 44.0 bits (105), Expect = 1e-06
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRA 44
          +D  +K  RG GF+TF     V+ ++    HEL   T+    A
Sbjct: 34 RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA 76

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

 Score = 78.0 bits (193), Expect = 4e-19
 Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRV-S 157
            K+FVG L  + + +DL+ YF++FG ++D  +     TG  RGFGF+ F +    ++V  
Sbjct: 12  GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71

Query: 158 RRSHEICGQQVAIDSA 173
           ++ H + G+ +    A
Sbjct: 72  QKEHRLDGRVIDPKKA 87

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

 Score = 42.9 bits (102), Expect = 3e-06
 Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRA 44
           D  +   RG GFI F  A SVE ++    H L G  +   +A
Sbjct: 45 MDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 23/178 (12%), Positives = 49/178 (27%), Gaps = 54/178 (30%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
                   +   F+ F S D     M  D     G ++ + R    +             
Sbjct: 43  LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA-------- 94

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                    K+F+G LP     + ++  
Sbjct: 95  ----------------------------------------HKLFIGGLPNYLNDDQVKEL 114

Query: 122 FSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRV--SRRSHEICGQQVAIDSAT 174
            + FG +    + K   TG  +G+ F  + +  V D+        ++  +++ +  A+
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 13/92 (14%), Positives = 30/92 (32%), Gaps = 9/92 (9%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-------KRTG-HRGFGFVTFAEEVVA 153
           ++++VG +P   T E +  +F+   R+  +           +    + F F+ F      
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 154 DRV-SRRSHEICGQQVAIDSATPLDDAGPSQN 184
            +  +       GQ + I           +  
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 9/47 (19%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRAT 45
           + KD  +   +G  F  +   +  +  +  ++  +LG   ++V RA+
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 76.2 bits (188), Expect = 4e-18
 Identities = 30/78 (38%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRV-S 157
            KIFVG LP   T   LR+YF  FG I +  V   ++TG  RG+GFVT A+   A+R   
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77

Query: 158 RRSHEICGQQVAIDSATP 175
             +  I G++  ++ A  
Sbjct: 78  DPNPIIDGRKANVNLAYL 95

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 2/66 (3%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
            D+ +   RG GF+T A   + E    D    + G    V+ A       R +      G
Sbjct: 51  TDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKP-RSLQTGFAIG 109

Query: 62  YGAYNA 67
               ++
Sbjct: 110 VSGPSS 115

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 77.8 bits (192), Expect = 6e-18
 Identities = 25/179 (13%), Positives = 54/179 (30%), Gaps = 34/179 (18%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
                   +   F+ F S D     M  D     G ++ + R    +         S   
Sbjct: 43  LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYV 102

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
            G  +  +  +                              K+F+G LP     + ++  
Sbjct: 103 PGVVSTVVPDS----------------------------AHKLFIGGLPNYLNDDQVKEL 134

Query: 122 FSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRV--SRRSHEICGQQVAIDSATP 175
            + FG +    + K   TG  +G+ F  + +  V D+        ++  +++ +  A+ 
Sbjct: 135 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV 193

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 53.1 bits (128), Expect = 7e-09
 Identities = 16/122 (13%), Positives = 37/122 (30%), Gaps = 11/122 (9%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-------KRTGH-RGFGFVTFAEEVVA 153
           ++++VG +P   T E +  +F+   R+  +           +    + F F+ F      
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 154 DR-VSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMY-GSLD 211
            + ++       GQ + I                            P   + +++ G L 
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH-KLFIGGLP 123

Query: 212 FD 213
             
Sbjct: 124 NY 125

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 9/52 (17%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD 50
           + KD  +   +G  F  +   +  +  +   +  +LG   ++V RA+    +
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197

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

 Score = 75.4 bits (185), Expect = 7e-18
 Identities = 26/118 (22%), Positives = 47/118 (39%), Gaps = 21/118 (17%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH-----RGFGFVTFA 148
           G S     +K+FVG LP +   +++   F RFG ++  +  K         +G+ F+ F 
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 149 EEVVADRV-SRRSHEICGQQVAIDSATP-----------LDDAGPSQNFMMNAAETFG 194
           EE     +      E     + + S T            L D+    +F+M++  + G
Sbjct: 61  EESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDS----DFVMDSGPSSG 114

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 24/176 (13%), Positives = 57/176 (32%), Gaps = 53/176 (30%)

Query: 4   DQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGY 62
           D  +  +R  G++ F SA+ +E  L +   ++ G+ + +++   ++              
Sbjct: 47  DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRD-------------- 92

Query: 63  GAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYF 122
                                               R  + +    L    T ++L+  F
Sbjct: 93  --------------------------------SKKVRAARTLLAKNLSFNITEDELKEVF 120

Query: 123 SRFGRILDVYVPKRTGH-RGFGFVTFAEEVVADRV--SRRSHEICGQQVAIDSATP 175
                I    +  + G  +G  ++ F  E  A++    ++  EI G+ V++     
Sbjct: 121 EDALEIR---LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 66.9 bits (164), Expect = 4e-14
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 4/97 (4%)

Query: 93  RGESSQRIG-KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-TG-HRGFGFVTFAE 149
             E S+      +F+G L    +  +L+   S      D+ V    TG +R FG+V F  
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFES 63

Query: 150 EVVADR-VSRRSHEICGQQVAIDSATPLDDAGPSQNF 185
               ++ +     ++ G ++ ++     D        
Sbjct: 64  AEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAAR 100

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 2/39 (5%)

Query: 11  RGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
           +GI +I F S    E  +      E+ G +V +     K
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 71.2 bits (175), Expect = 3e-16
 Identities = 30/91 (32%), Positives = 45/91 (49%), Gaps = 9/91 (9%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTG-HRGFGFVTFAEEVVADR- 155
             KI V  +P +A   ++R  FS FG +  V +PK    TG HRGFGFV F  +  A + 
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74

Query: 156 --VSRRSHEICGQQVAIDSATPLDD--AGPS 182
                 S  + G+++ ++ A       +GPS
Sbjct: 75  FNALCHSTHLYGRRLVLEWADSEVTVQSGPS 105

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 1  MPKDQ-GSKAHRGIGFITFASADSVEN---LMVDTHELGGSTVVVDRATPKED 49
          +PK   G+ AHRG GF+ F +    +     +  +  L G  +V++ A  +  
Sbjct: 47 LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT 99

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 72.6 bits (179), Expect = 4e-16
 Identities = 26/157 (16%), Positives = 50/157 (31%), Gaps = 48/157 (30%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDTHE--LGGSTVVVDRATPKEDDFRPVGRMSHG 60
           + Q     +G  F+TF +  +        H   +        +  P + +          
Sbjct: 39  RSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE---------- 88

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
                                             +++    +K+F+G + ++ T  D+R 
Sbjct: 89  ----------------------------------KNNAVEDRKLFIGMISKKCTENDIRV 114

Query: 121 YFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADR 155
            FS FG+I +  + +   G  RG  FVTF    +A  
Sbjct: 115 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQT 151

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 68.8 bits (169), Expect = 9e-15
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 5/59 (8%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG---HRGFGFVTFAEEVVADRV 156
           K+FVG++P+  + +DLR  F ++G + ++ V   +       +G  FVTF     A   
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 4/100 (4%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADRVSRR- 159
           K+F+G L +E   + L+  F + G I +V + K RT   RGF F+TF     A   ++  
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68

Query: 160 -SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGG 198
               + G+ + ++ A         +     ++      G 
Sbjct: 69  NGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 72.7 bits (179), Expect = 2e-15
 Identities = 31/185 (16%), Positives = 59/185 (31%), Gaps = 54/185 (29%)

Query: 1   MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKEDDFRPVGR 56
           +P  + +   R   +I   S +     VE L  +  ++ G T+V   + P E        
Sbjct: 150 LPSLRFNT-SRRFAYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNPLEKS------ 200

Query: 57  MSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAE 116
                                               R +S+   G++I +  L  E   E
Sbjct: 201 -----------------------------------KRTDSATLEGREIMIRNLSTELLDE 225

Query: 117 D-LRRYFSRFGRILDVYVPKR---TGH-RGFGFVTFAEEVVADR-VSRRSHEICGQQVAI 170
           + LR  F  FG I  + +P             F+ F  +  A+R +      +  +++++
Sbjct: 226 NLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISV 285

Query: 171 DSATP 175
             A  
Sbjct: 286 SLADK 290

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 64.2 bits (157), Expect = 2e-12
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSRRSH- 161
           + V  LP+      + +YF   G I+ V V      +  F  + FA    A     ++H 
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103

Query: 162 EICGQQVAIDSAT 174
            +   ++ +   T
Sbjct: 104 VVGQNEIIVSHLT 116

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 59.6 bits (145), Expect = 8e-11
 Identities = 14/96 (14%), Positives = 35/96 (36%), Gaps = 5/96 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRI-LDVYVPK-RTG-HRGFGFVTFAEEVVADRVSRR 159
            +++   P   T  ++R        + L + +P  R    R F ++    +  A     +
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178

Query: 160 SH--EICGQQVAIDSATPLDDAGPSQNFMMNAAETF 193
            +  +I G  +    + PL+ +  + +  +   E  
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIM 214

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 68.5 bits (168), Expect = 3e-15
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEV 151
              +R  + +F  +L       DL  +FS  G++ DV +   + +   +G  +V F E  
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78

Query: 152 VADR-VSRRSHEICGQQVAIDSATP 175
                +      + G  + + ++  
Sbjct: 79  SVPLAIGLTGQRLLGVPIIVQASQA 103

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 42.7 bits (101), Expect = 9e-06
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKE 48
           +  D+ S+  +GI ++ F    SV   + +    L G  ++V  +  ++
Sbjct: 57  IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK 105

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 67.7 bits (166), Expect = 4e-15
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 90  FYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVT 146
             G          K+F+G++P+    +DL+  F  FG+I ++ V   + TG H+G  F+T
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 147 FAEEVVADR 155
           + E   A +
Sbjct: 62  YCERESALK 70

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 70.8 bits (174), Expect = 7e-15
 Identities = 22/186 (11%), Positives = 46/186 (24%), Gaps = 52/186 (27%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +   + +   +G GF  +   DS       +    LG  T+ V      +          
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL--------- 177

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEAT-AED 117
                                                      + + V RLP      + 
Sbjct: 178 ----------------------------------TPALLH--SRCLCVDRLPPGFNDVDA 201

Query: 118 LRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADRVSRRSH--EICGQQVAIDSA 173
           L R  S         +   + G  +GF  + +    +A+   +++    + G  + +   
Sbjct: 202 LCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261

Query: 174 TPLDDA 179
            P    
Sbjct: 262 APGPPG 267

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 60.4 bits (147), Expect = 4e-11
 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 3/63 (4%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVV 152
             Q     + V  LP   T +        FG +   ++    RTG  +G+GF  + ++  
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 153 ADR 155
           A R
Sbjct: 150 AAR 152

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 56.1 bits (136), Expect = 1e-09
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVV 152
             E   R  +KI +  LP + T +++    S +  +   +V K   ++G  FVT      
Sbjct: 14  HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK---YKGTAFVTLLNGEQ 69

Query: 153 ADRVSRRSH--EICGQQVAIDSATP 175
           A+      H   +  +++++     
Sbjct: 70  AEAAINAFHQSRLRERELSVQLQPT 94

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 66.9 bits (164), Expect = 8e-15
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEV 151
           G   SS +   K+ VG +    T ++LR  F  +G +++  +      + + FV      
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAE 55

Query: 152 VADRVSRR--SHEICGQQVAIDSATP 175
            A    R   + E  G+++ +  +T 
Sbjct: 56  DAVEAIRGLDNTEFQGKRMHVQLSTS 81

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 66.5 bits (163), Expect = 1e-14
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 5/90 (5%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTF 147
            G           + V  L    + + LRR F ++GR+ DVY+P+   T   RGF FV F
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62

Query: 148 AEEVVADRVSRR--SHEICGQQVAIDSATP 175
            +   A          E+ G+++ +  A  
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRVQVARY 92

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

 Score = 66.1 bits (162), Expect = 1e-14
 Identities = 26/93 (27%), Positives = 49/93 (52%), Gaps = 9/93 (9%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           G S      K+F+G LP+EAT +++R  F ++G++L+  + K      +GFV   ++  A
Sbjct: 1   GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK-----NYGFVHIEDKTAA 55

Query: 154 DRVSRRSH--EICGQQVAIDSATPLDDA--GPS 182
           +   R  H  ++ G  + ++++     A  GPS
Sbjct: 56  EDAIRNLHHYKLHGVNINVEASKNKSKASSGPS 88

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 67.2 bits (164), Expect = 2e-14
 Identities = 29/142 (20%), Positives = 53/142 (37%), Gaps = 12/142 (8%)

Query: 36  GSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGE 95
            +T  VD AT +    +   + ++            AT+   +   + + H         
Sbjct: 16  TTTEAVDAATAE----KVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHM----HR 67

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
            S  +  K++VG L       +L R F  +G +  V+V +     GF FV F +   A  
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--PPGFAFVEFEDPRDAAD 125

Query: 156 VSRRSH--EICGQQVAIDSATP 175
             R      +CG +V ++ +  
Sbjct: 126 AVRELDGRTLCGCRVRVELSNG 147

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 66.2 bits (162), Expect = 2e-14
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 11/95 (11%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRVS 157
           GK +F+  L  ++  E L     +FG +  V V     T H +G  F  F  +  A +  
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74

Query: 158 RRSH--------EICGQQVAIDSATPLDDAGPSQN 184
             +         ++ G+Q+ +D A   D+A    +
Sbjct: 75  AAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 8/57 (14%), Positives = 22/57 (38%), Gaps = 8/57 (14%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--------VDTHELGGSTVVVDRATPKED 49
           +     ++  +G  F  F + ++ +  +            +L G  + VD A  +++
Sbjct: 47  VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

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

 Score = 66.3 bits (162), Expect = 3e-14
 Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFA 148
           G    S    + ++VG L +E   + L   F  FG I D+ +P    T  HRGF FV F 
Sbjct: 54  GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113

Query: 149 EEVVAD 154
               A 
Sbjct: 114 LAEDAA 119

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 65.3 bits (160), Expect = 3e-14
 Identities = 32/100 (32%), Positives = 45/100 (45%), Gaps = 7/100 (7%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGF 144
           GS    G +S     K+FVG L  +   + L + FS++G+I +V V K   T   RGFGF
Sbjct: 1   GSSGSSGMASD--EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGF 58

Query: 145 VTFAEEVVADRVSRR--SHEICGQQVAIDSATPLDDAGPS 182
           VTF     A           + G+Q+ +D A    D    
Sbjct: 59  VTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSG 98

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 39.9 bits (94), Expect = 6e-05
 Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          + KD+ ++  RG GF+TF + D  ++ M  ++   + G  + VD+A    D
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

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

 Score = 65.4 bits (160), Expect = 4e-14
 Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 4/98 (4%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGF 144
            GS      S+     K+F+  LP   T E+L       G + D+ +   R G  +G  +
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAY 62

Query: 145 VTFAEEVVADRVSRR--SHEICGQQVAIDSATPLDDAG 180
           V +  E  A +   +     I    + +  +     +G
Sbjct: 63  VEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSSG 100

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

 Score = 65.4 bits (160), Expect = 4e-14
 Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 7/99 (7%)

Query: 84  YDHPGSFYGRGESSQRI----GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG 138
           + H      RG           K++ V  +P      DLR+ F +FG+ILDV +     G
Sbjct: 8   HHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 67

Query: 139 HRGFGFVTFAEEVVADRVSRRSH--EICGQQVAIDSATP 175
            +GFGFVTF     ADR   + H   + G+++ +++AT 
Sbjct: 68  SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 106

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

 Score = 64.2 bits (157), Expect = 7e-14
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
            S     KIFVG +    T+++LR  F R GR+++  V      + + FV   +E  A  
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV-----VKDYAFVHMEKEADAKA 58

Query: 156 VSRRSH--EICGQQVAIDSATP 175
              + +  E+ G+++ ++ +T 
Sbjct: 59  AIAQLNGKEVKGKRINVELSTK 80

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 64.2 bits (157), Expect = 8e-14
 Identities = 35/102 (34%), Positives = 55/102 (53%), Gaps = 6/102 (5%)

Query: 88  GSFYGRGESSQRI-GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGHRGFGFV 145
           GS    G S  +   K++ V  +P      DLR+ F +FG+ILDV +     G +GFGFV
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 60

Query: 146 TFAEEVVADRVSRRSH--EICGQQVAIDSATP--LDDAGPSQ 183
           TF     ADR   + H   + G+++ +++AT   + ++GPS 
Sbjct: 61  TFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.3 bits (157), Expect = 9e-14
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
            +     +I+VG LP +   +D+   F ++G I D+ +  R G   F FV F +   A+ 
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 76

Query: 156 VSRRSH--EICGQQVAIDSATP 175
                   +  G ++ ++    
Sbjct: 77  AVYGRDGYDYDGYRLRVEFPRS 98

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 64.2 bits (157), Expect = 1e-13
 Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 7/100 (7%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGF 144
           GS    G ++ +  + ++VG L +E   + L   F  FG I D+ +P    T  HRGF F
Sbjct: 1   GSSGSSGMATTK--RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 58

Query: 145 VTFAEEVVADRVSRRSH--EICGQQVAIDSATPLDDAGPS 182
           V F     A       +  E+ G+ + ++ A P+      
Sbjct: 59  VEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESG 98

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          +P D  ++ HRG  F+ F  A+     +  ++  EL G T+ V+ A P   
Sbjct: 44 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 64.2 bits (157), Expect = 1e-13
 Identities = 24/96 (25%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFA 148
                       I V  L ++    DL+  F  FG I  +Y+   K TG  +GF F++F 
Sbjct: 6   SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65

Query: 149 EEVVADRVSRR--SHEICGQQVAIDSATPLDDAGPS 182
               A R              + ++ A P  ++GPS
Sbjct: 66  RREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 24/160 (15%), Positives = 44/160 (27%), Gaps = 53/160 (33%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           + +D  +    G  F+ F S    +    +++   +    + V  A P            
Sbjct: 35  IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG----------- 83

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                                        ++V  LP+  T + L
Sbjct: 84  -------------------------------------GESIKDTNLYVTNLPRTITDDQL 106

Query: 119 RRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADR 155
              F ++G I+   +   K TG  RG  FV + +   A  
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 60.7 bits (148), Expect = 8e-12
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS 157
              + V  LPQ+ T  +L   F   G I    +    +TG   G+ FV F  E+ + R  
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 158 RR--SHEICGQQVAIDSATPLDDAGPSQN 184
           +      +  +++ +  A P  ++    N
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGESIKDTN 91

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 63.3 bits (155), Expect = 1e-13
 Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVAD 154
           + ++VG L +E   + L   F  FG I D+ +P    T  HRGF FV F     A 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 29/161 (18%), Positives = 53/161 (32%), Gaps = 53/161 (32%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           + +D+ +    G GF+ +      E     ++   L   T+ V  A P     R      
Sbjct: 34  LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIR------ 87

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                                        ++V  LP+  T ++L
Sbjct: 88  ------------------------------------------DANLYVSGLPKTMTQKEL 105

Query: 119 RRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRV 156
            + FS++GRI+   +   + TG  RG GF+ F + + A+  
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV 156
            + V  LPQ  T E+ R  F   G I    +   K TG   G+GFV + +   A++ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 63.8 bits (156), Expect = 1e-13
 Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 7/97 (7%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEV 151
            ES     +K+FVG L ++ + ED+ R F  FG I +  V +   G  +G  FV F+   
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHT 67

Query: 152 VADRVSRRSH-----EICGQQVAIDSATPLDDAGPSQ 183
            A       H           + +  A    ++GPS 
Sbjct: 68  EAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSS 104

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 63.4 bits (154), Expect = 2e-13
 Identities = 25/85 (29%), Positives = 34/85 (40%), Gaps = 1/85 (1%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           G S    G  + V  LP     E L  YF    R     V         G +TF E   A
Sbjct: 1   GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADA 60

Query: 154 DRV-SRRSHEICGQQVAIDSATPLD 177
           +RV ++  HE+ G Q+++  A P  
Sbjct: 61  ERVLAQADHELHGAQLSLRPAPPRA 85

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

 Score = 62.7 bits (153), Expect = 3e-13
 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
           GS     +  +    ++FV   P +    +L   F  FG + +V +       GF FV F
Sbjct: 18  GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-----GFAFVEF 72

Query: 148 AEEVVADRVSRRSH--EICGQQVAIDSATP 175
            E   A +     H      Q + +  +  
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKL 102

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 62.3 bits (152), Expect = 3e-13
 Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAE 149
           G   + +   + +FVG L      E L   F + G +  V + K R G  + FGFV F  
Sbjct: 7   GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKH 66

Query: 150 EVVADR 155
                 
Sbjct: 67  PESVSY 72

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

 Score = 62.3 bits (152), Expect = 4e-13
 Identities = 15/91 (16%), Positives = 33/91 (36%), Gaps = 11/91 (12%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVPK--RTGH-RGFGFVTFA 148
           G         I +  +      + +    S +    + ++ + K  +T   RGF FV  +
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 149 EEVVADRV------SRRSHEICGQQVAIDSA 173
             + A ++           +I G+ + +D A
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 62.8 bits (153), Expect = 4e-13
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 99  RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR 158
            + + +++  LP + TAE++   F ++G I  + V      RG  +V + +   A     
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVD 65

Query: 159 R--SHEICGQQVAIDSATP 175
                 +  + + +     
Sbjct: 66  HLSGFNVSNRYLVVLYYNA 84

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 62.2 bits (152), Expect = 5e-13
 Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 5/95 (5%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEE 150
           G S      ++FV  L   ++ EDL + FS +G + +++ P    T   +GF FVTF   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 151 VVADRVSRR--SHEICGQQVAIDSATPLDDAGPSQ 183
             A +           G+ + +  +T   +A  S 
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 61.9 bits (151), Expect = 5e-13
 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           G S      K+++G L    TA+DLR+ F      L   V       G+ FV + ++  A
Sbjct: 1   GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWA 57

Query: 154 DRVSRR---SHEICGQQVAIDSATPLDD--AGPS 182
            R         E+ G+ + +D +       +GPS
Sbjct: 58  IRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 62.1 bits (151), Expect = 6e-13
 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 11/102 (10%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPK----RTGHRGFGFVTFAEEVVADR-- 155
           ++F+G +P+    E++    ++    +LDV V      +  +RGF FV +     A    
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 156 --VSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGG 195
             +     ++ G Q+A+D A P  D    ++ M   +    G
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAEPEID--VDEDVMETVSGPSSG 109

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKED 49
                   +RG  F+ + S  +       LM    +L G  + VD A P+ D
Sbjct: 42 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 61.9 bits (151), Expect = 6e-13
 Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVV 152
            GE +     ++FVG LP + T E++R+ F ++G+  +V++ K    +GFGF+      +
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTL 63

Query: 153 ADRVSRRSH--EICGQQVAIDSATP 175
           A+          + G+Q+ +  A  
Sbjct: 64  AEIAKVELDNMPLRGKQLRVRFACH 88

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 61.4 bits (150), Expect = 6e-13
 Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEE 150
            + I+VG +   ATAE+L  +F   G +  V +   K +GH +GF ++ F+++
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK 58

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

 Score = 61.6 bits (150), Expect = 8e-13
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 8/93 (8%)

Query: 86  HPGSFYGRGESSQRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGF 144
           H     G       +  ++F+G LP +  + EDL R FS +G I+ + +        FGF
Sbjct: 7   HHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGF 61

Query: 145 VTFAEEVVADRVSRRSH--EICGQQVAIDSATP 175
           + F                   G+++ ++ ++ 
Sbjct: 62  IQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS 94

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

 Score = 61.5 bits (150), Expect = 8e-13
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV--SRRS 160
           K++VG L   A   +L R FS +G +  V++ +     GF FV F +   A+        
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGLDG 59

Query: 161 HEICGQQVAIDSATP 175
             ICG +V ++ +T 
Sbjct: 60  KVICGSRVRVELSTG 74

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

 Score = 62.1 bits (151), Expect = 1e-12
 Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFG 143
               YGR          + V  L    + + LRR F ++GR+ DVY+P+   T   RGF 
Sbjct: 33  GSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 92

Query: 144 FVTFAEEVVADRVSRR--SHEICGQQVAIDSATP 175
           FV F ++  A+          + G+++ +  A  
Sbjct: 93  FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 126

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 61.7 bits (150), Expect = 1e-12
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEE 150
           + ++VG +   +TA+DL  +FS  G I  + +   K +GH +G+ ++ FAE 
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER 88

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 61.1 bits (149), Expect = 1e-12
 Identities = 27/101 (26%), Positives = 41/101 (40%), Gaps = 6/101 (5%)

Query: 88  GSFYGRGESSQR-IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH-RGFGFV 145
           GS    G+   R     ++V  L      E LR+ FS FG I    V    G  +GFGFV
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFV 60

Query: 146 TFAEEVVADR--VSRRSHEICGQQVAIDSATPLDD--AGPS 182
            F+    A +         +  + + +  A   ++  +GPS
Sbjct: 61  CFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGPS 101

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 61.1 bits (149), Expect = 1e-12
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           K ++V  L    + E + + F+         V K    R + FV F+    A    +  +
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALN 72

Query: 162 --EICGQQVAIDSATPLDD--AGPS 182
              + G  + +  A P+D   +GPS
Sbjct: 73  GKVLDGSPIEVTLAKPVDKDSSGPS 97

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

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 96  SSQRIGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
            +     ++F+G LP +  + EDL R FS +G I+ + +        FGF+ F       
Sbjct: 5   HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVR 59

Query: 155 RVSRRSH--EICGQQVAIDSATP 175
                       G+++ ++ ++ 
Sbjct: 60  DAIECESQEMNFGKKLILEVSSS 82

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 64.3 bits (157), Expect = 2e-12
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVT 146
             SF   GE +     ++FVG LP + T ED +R F R+G   +V++ +    RGFGF+ 
Sbjct: 8   IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR---DRGFGFIR 64

Query: 147 FAEEVVADRV 156
                +A+  
Sbjct: 65  LESRTLAEIA 74

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 62.8 bits (153), Expect = 4e-12
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRTGHRGFGFVTFAEEVVADRV 156
           G  + V  L    + E L + FS+FG +    V    R    G GFV FA +  A + 
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 60.2 bits (147), Expect = 2e-12
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTG-HRGFGFVTFAEEVVADRVSR 158
           K+ +GRL +  T + +   FS +G+I  + +P         +G+ +V F     A++  +
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 159 RSH--EICGQQVAIDSATP 175
                +I GQ++   +   
Sbjct: 66  HMDGGQIDGQEITATAVLA 84

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 62.2 bits (151), Expect = 2e-12
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFA 148
                       + V  L    + + LRR F ++GR+ DVY+P+   T   RGF FV F 
Sbjct: 61  HHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 120

Query: 149 EEVVADRVSRR--SHEICGQQVAIDSATP 175
           ++  A+          + G+++ +  A  
Sbjct: 121 DKRDAEDAMDAMDGAVLDGRELRVQMARY 149

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 9/116 (7%)

Query: 93  RGESSQRIGK-KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEE 150
           R  S ++ G   IF+  L +    + L   FS FG IL   V       +G+GFV F  +
Sbjct: 94  RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQ 153

Query: 151 VVADRVSRRSH--EICGQQVAIDSATPLDDA-----GPSQNFMMNAAETFGGYGGP 199
             A+R   + +   +  ++V +       +        ++ F       + G  G 
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGR 209

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 3/56 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV 156
           ++VG L  + T   L   FS  G IL + V     T    G+ +V F +   A+R 
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73

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

 Score = 60.4 bits (147), Expect = 3e-12
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS 157
           G  +FV  + +EA  ++++  F  +G I ++++   +RTG  +G+  V +     A    
Sbjct: 26  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85

Query: 158 RR--SHEICGQQVAIDSATP 175
                 EI GQ + +D    
Sbjct: 86  EALNGAEIMGQTIQVDWCFV 105

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

 Score = 60.3 bits (147), Expect = 3e-12
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS 157
           G  +FV  + +EAT ED+   F+ +G I ++++   +RTG  +G+  V +     A    
Sbjct: 23  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82

Query: 158 RR--SHEICGQQVAIDSATP 175
                 ++ GQ +++D    
Sbjct: 83  EGLNGQDLMGQPISVDWCFV 102

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 59.6 bits (145), Expect = 4e-12
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 6/86 (6%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH-RGFGFVTFAEEV 151
                 R  + +    L    T ++L+  F     I  V    + G  +G  ++ F  E 
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEA 64

Query: 152 VADRVSRR--SHEICGQQVAIDSATP 175
            A++        EI G+ V++     
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGE 90

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 59.5 bits (145), Expect = 4e-12
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADR 155
              + V  L    T  DLR  FS++G I DV +    ++   RGF FV F     A  
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 60.5 bits (147), Expect = 4e-12
 Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 5/90 (5%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTF 147
           +    ++      + V  L    T  DLR  FS++G I DV +   +++   RGF FV F
Sbjct: 36  HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 95

Query: 148 AEEVVADRVSRRSH--EICGQQVAIDSATP 175
                A     R++  E+ G+++ +D +  
Sbjct: 96  ENVDDAKEAKERANGMELDGRRIRVDFSIT 125

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 59.6 bits (145), Expect = 5e-12
 Identities = 15/88 (17%), Positives = 41/88 (46%), Gaps = 5/88 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR 158
           + +++G +P + T E +    S  G ++++ +    +TG  +G+ F+ F +   +    R
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 159 R--SHEICGQQVAIDSATPLDDAGPSQN 184
               +++  + +    ++  D +G S  
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDISGVSLE 90

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 6/54 (11%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKEDD 50
          M  D  +   +G  FI F   +S    V NL  + ++LG   +    ++  +  
Sbjct: 34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNL--NGYQLGSRFLKCGYSSNSDIS 85

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 60.1 bits (146), Expect = 5e-12
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS 157
           G  +FV  + +EAT ED+   F+ +G I ++++   +RTG  +G+  V +     A    
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

Query: 158 RRSH--EICGQQVAIDSATP 175
              +  ++ GQ +++D    
Sbjct: 82  EGLNGQDLMGQPISVDWCFV 101

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 59.2 bits (144), Expect = 5e-12
 Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 13/98 (13%)

Query: 94  GESSQRIGKK----IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAE 149
           G S +R   +    ++V     + T   LR  FS FG I+D+ +      R   FVT+ +
Sbjct: 4   GSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP---PRNCAFVTYEK 58

Query: 150 EVVADRVSRRSH--EICGQQVAIDSAT--PLDDAGPSQ 183
              AD+     +  ++   Q+ ++ A   P+ D+GPS 
Sbjct: 59  MESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPSS 96

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.6 bits (145), Expect = 6e-12
 Identities = 26/94 (27%), Positives = 48/94 (51%), Gaps = 6/94 (6%)

Query: 88  GSFYGRGESSQR-IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFG 143
           GS    G  S+R     ++VG L ++ +   L   F + G +++ ++PK   TG H+G+G
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 144 FVTFAEEVVADRVSR--RSHEICGQQVAIDSATP 175
           FV F  E  AD   +     ++ G+ + ++ A+ 
Sbjct: 61  FVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA 94

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           MPKD+ +  H+G GF+ F S +  +  +  +D  +L G  + V++A+    +       S
Sbjct: 47  MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS---GPS 103

Query: 59  HG 60
            G
Sbjct: 104 SG 105

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 59.6 bits (145), Expect = 7e-12
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGHRGFGFVTFAEEVVADR 155
             IF+  L +    + L   FS FG IL   V     G +G+GFV F  +  A+R
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 60

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

 Score = 59.3 bits (144), Expect = 8e-12
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 5/73 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS 157
            K++   RL        L+    ++G + +V +    RT  H G   V F     A    
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 158 RRSH--EICGQQV 168
           +  H   + G  +
Sbjct: 66  KNLHLTSVMGNII 78

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 59.8 bits (145), Expect = 8e-12
 Identities = 21/94 (22%), Positives = 33/94 (35%), Gaps = 7/94 (7%)

Query: 65  YNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSR 124
           Y+ Y   A           +  P       +      + + V  +P       LR+ F R
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDV----LRNLMVNYIPTTVDEVQLRQLFER 65

Query: 125 FGRILDVYVP--KRTGH-RGFGFVTFAEEVVADR 155
           +G I  V +   + T   RG+GFV F     A +
Sbjct: 66  YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

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

 Score = 59.0 bits (143), Expect = 9e-12
 Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFAEEVVADR 155
               + +++   P +AT +D++ +    G++L++ + +      +G  FV F     A +
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 156 -VSRRSHEICGQQVAIDSA 173
            V     +     + I   
Sbjct: 68  FVETPGQKYKETDLLILFK 86

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.8 bits (143), Expect = 9e-12
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR 155
              ++V  LP   T  DL R FS++G+++ V +   K T   +G  F+ F ++  A  
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 58.4 bits (142), Expect = 1e-11
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTGH-RGFGFVTFAEEVVADR-VSRR 159
            +F+G L    +  +L+   S      D+ V   RTG  R FG+V F      ++ +   
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78

Query: 160 SHEICGQQVAIDSATPLDD 178
             ++ G ++ ++     D 
Sbjct: 79  GLKVFGNEIKLEKPKGRDG 97

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 57.9 bits (141), Expect = 1e-11
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGH-RGFGFVTFAEEVVADRVSRR 159
            +FVG L      E LR  F  F   L  +V    +TG  RG+GFV+F  +  A      
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 160 SH--EICGQQVAIDSATP 175
               ++ G+ + I+ A  
Sbjct: 63  MQGQDLNGRPLRINWAAK 80

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

 Score = 58.3 bits (142), Expect = 1e-11
 Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEE 150
           + I+VG L   AT+E ++  FS+FG++ +V +   + T   +GFGFV   EE
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE 53

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 98  QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV 156
           + I  ++F+G L        D+   FS++GR+    V     H+G+ FV ++ E  A   
Sbjct: 24  KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----HKGYAFVQYSNERHARAA 78

Query: 157 SRRSH--EICGQQVAIDSATP 175
               +   + GQ + I+ A  
Sbjct: 79  VLGENGRVLAGQTLDINMAGE 99

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 57.9 bits (141), Expect = 1e-11
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADR 155
              +++  L    T +DL +    +G+I+       K T   +G+GFV F     A +
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 58.4 bits (142), Expect = 1e-11
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           K +FV  L    T E L + FS+FG++  V   K      + F+ F E   A +     +
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-----DYAFIHFDERDGAVKAMEEMN 66

Query: 162 --EICGQQVAIDSATPLDD 178
             ++ G+ + I  A P D 
Sbjct: 67  GKDLEGENIEIVFAKPPDQ 85

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 102 KKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
             I++  L ++   ++L++     FSRFG+ILD+ V +    RG  FV F E   A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66

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

 Score = 58.1 bits (141), Expect = 2e-11
 Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 5/67 (7%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH-- 161
            ++G +P  AT  DL   F  FG ILD         +G  F+ +     A          
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHYP---EKGCCFIKYDTHEQAAVCIVALANF 86

Query: 162 EICGQQV 168
              G+ +
Sbjct: 87  PFQGRNL 93

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 57.7 bits (140), Expect = 2e-11
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
             ++VG L    T  DLR +F +FG I  + V +R   +   F+ FA    A+  + +S 
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR---QQCAFIQFATRQAAEVAAEKSF 69

Query: 162 ---EICGQQV 168
               + G+++
Sbjct: 70  NKLIVNGRRL 79

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 57.9 bits (141), Expect = 2e-11
 Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 5/88 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR 158
             ++VG L    T + LR  F  FG+I ++ +     TG  +G+GF+TF++   A R   
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 159 R--SHEICGQQVAIDSATPLDDAGPSQN 184
           +    E+ G+ + +   T   D G   +
Sbjct: 66  QLNGFELAGRPMRVGHVTERLDGGSGPS 93

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 5/99 (5%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVV 152
           +  R  + +FVG +P EAT E L+  FS  G ++   +   + TG  +G+GF  + ++  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 153 ADRVSRR--SHEICGQQVAIDSATPLDDAGPSQNFMMNA 189
           A    R     E  G+ + +D+A    +    ++    A
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 59.5 bits (144), Expect = 2e-11
 Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 5/108 (4%)

Query: 73  TRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVY 132
           TR A      + +        G      G  +FV  + +EA  ++++  F  +G I +++
Sbjct: 44  TREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH 103

Query: 133 VP--KRTG-HRGFGFVTFAEEVVADRVSRRSH--EICGQQVAIDSATP 175
           +   +RTG  +G+  V +     A       +  EI GQ + +D    
Sbjct: 104 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 151

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.0 bits (140), Expect = 3e-11
 Identities = 15/84 (17%), Positives = 27/84 (32%), Gaps = 6/84 (7%)

Query: 102 KKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS 157
           + + +  +  E   E L+       S  G ILD+ V     + G  ++ FA +  A    
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFV 89

Query: 158 RRSH--EICGQQVAIDSATPLDDA 179
                    G  + I  +      
Sbjct: 90  EAFQGYPFQGNPLVITFSETPQSQ 113

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 57.7 bits (140), Expect = 4e-11
 Identities = 31/101 (30%), Positives = 48/101 (47%), Gaps = 7/101 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRVSRR 159
            +FVG L  E T ED++  F+ FGRI D  V     TG  +G+GFV+F  +  A+   ++
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 160 SH--EICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGG 198
                + G+Q+  + AT    A  S     +  +  G   G
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTY--ESNTKQSGPSSG 115

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 56.4 bits (137), Expect = 5e-11
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADRVSRR 159
            +FVG L  E T   +   F+ FGRI D  V     TG  +G+GFV+F  +  A+   ++
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 160 SH--EICGQQVAIDSATP 175
                + G+Q+  + AT 
Sbjct: 68  MGGQWLGGRQIRTNWATR 85

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 56.5 bits (137), Expect = 6e-11
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 10/66 (15%)

Query: 92  GRGESSQRIG-------KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGF 144
           G   SS +IG        +++VG L    +   L R F RFG I  +   K      F +
Sbjct: 1   GSSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK---GDSFAY 57

Query: 145 VTFAEE 150
           + +   
Sbjct: 58  IQYESL 63

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 56.6 bits (137), Expect = 7e-11
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH-- 161
           ++ G +    T + +R+ FS FG+I+++ V      +G+ FV F+    A       +  
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---EKGYSFVRFSTHESAAHAIVSVNGT 84

Query: 162 EICGQQVAIDSATP 175
            I G  V       
Sbjct: 85  TIEGHVVKCYWGKE 98

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

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH-RGFGFVTFAEEVV 152
           G S      +IFV  LP + T + L+  F+  G +L   +    G  +G G V F    V
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV 60

Query: 153 ADR 155
           A+R
Sbjct: 61  AER 63

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSRR 159
           +++VG L    T + LR  F  FGRI  + +     TG  +G+GF+TF++   A +   +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 160 --SHEICGQQVAIDSATPLDD 178
               E+ G+ + +   T   D
Sbjct: 88  LNGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
           +  D  +   +G GFITF+ ++  +  +  ++  EL G  + V   T + D
Sbjct: 58  LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 55.8 bits (135), Expect = 1e-10
 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTFAEE 150
            G +    G K+ V  L    +  D++  F+ FG +    V   R+G   G   V F  +
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 80

Query: 151 VVADR 155
             A +
Sbjct: 81  ADALK 85

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

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 5/89 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TG-HRGFGFVTFAEEVVADRVS 157
            K +++  L    T  DL   F+RF       +  R  TG  RG  F+TF  + +A +  
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 158 RRSH--EICGQQVAIDSATPLDDAGPSQN 184
              +  ++ G+ + I+            +
Sbjct: 85  HLVNGYKLYGKILVIEFGKNKKQRSSGPS 113

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTFAEE 150
            G      G K+ V  L    +  D++  F+ FG +    V   R+G   G   V F   
Sbjct: 27  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERR 86

Query: 151 VVADRVSRRSH--EICGQQVAIDSATP 175
             A +  ++     + G+ + I     
Sbjct: 87  ADALKAMKQYKGVPLDGRPMDIQLVAS 113

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 9/92 (9%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-TGH-RGFGFV 145
           GS      S +   K + +  L   AT E L+  F +      + VP+   G  +G+ F+
Sbjct: 4   GSSGNSTWSGE--SKTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGKSKGYAFI 58

Query: 146 TFAEEVVADRVSRR--SHEICGQQVAIDSATP 175
            FA    A          EI G+ + ++   P
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRLELQGP 90

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGHRGFGFVTFAEEVVADR 155
           + ++VG L ++ T   + + FS+ G      +    T +  + FV F E   A  
Sbjct: 16  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 70

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

 Score = 55.1 bits (133), Expect = 3e-10
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFA 148
           G  +F+  LPQE T  DL   F  FG ++   V++ K+T   + FGFV+F 
Sbjct: 40  GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFD 90

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGH-RGFGFVTFAEEVVADR 155
           G  +F+  LPQE   +DL + F  FG ++   V++ K+T   + FGFV++   V A  
Sbjct: 25  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 55.2 bits (134), Expect = 6e-10
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADRVSRR 159
           + ++VG L +  T + L++YF   G I ++ +   +   +  + FV + +   A+   + 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 160 --SHEICGQQVAIDSATP 175
               +I    V I+ A  
Sbjct: 61  LNGKQIENNIVKINWAFQ 78

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 55.2 bits (134), Expect = 7e-10
 Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 5/89 (5%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGH-RGFGFVTF 147
           +   +SS      +FVG L      E LR  F  F   L  +V     TG  RG+GFV+F
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136

Query: 148 AEEVVADR--VSRRSHEICGQQVAIDSAT 174
             +  A     S +  ++ G+ + I+ A 
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINWAA 165

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 54.0 bits (130), Expect = 6e-10
 Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 3/64 (4%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEV 151
           G   SS R    I    LP    A +++  FSRFG +  V +P+         V F E +
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---GGITAIVEFLEPL 57

Query: 152 VADR 155
            A +
Sbjct: 58  EARK 61

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 54.1 bits (130), Expect = 7e-10
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 13/92 (14%)

Query: 96  SSQRIGKK--IFVGRLPQEATAEDLRR---YFSRFGRILDVYVPKRT------GHRGFGF 144
           +S R+ +K  +FV  L Q     ++ +   YF +FG+I  V +   T      G     +
Sbjct: 8   ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAY 67

Query: 145 VTFAEEVVADRVSRRSH--EICGQQVAIDSAT 174
           VT+     A R  +  +   + G+ +     T
Sbjct: 68  VTYIRSEDALRAIQCVNNVVVDGRTLKASLGT 99

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 4/81 (4%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTFAEEVVADRVSR 158
              +++  LP     ++L      FG+++   + +  +G  RG GF         + V  
Sbjct: 25  PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 84

Query: 159 R--SHEICGQQVAIDSATPLD 177
                 I           PL 
Sbjct: 85  HFNGKFIKTPPGVSAPTEPLL 105

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 54.9 bits (132), Expect = 1e-09
 Identities = 17/143 (11%), Positives = 38/143 (26%), Gaps = 16/143 (11%)

Query: 8   KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAY 65
              +    +  A  +  +  M  ++ H+L G  + +  +  +       G+   G    Y
Sbjct: 38  FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDY 97

Query: 66  NAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF 125
                   +            P                + +  +P   + EDL+  FS  
Sbjct: 98  GNSPLHRFKKPGSKNFQNIFPPS-------------ATLHLSNIPPSVSEEDLKVLFSSN 144

Query: 126 GRILDVYVPKRTGHRGFGFVTFA 148
           G ++          R    +   
Sbjct: 145 GGVVK-GFKFFQKDRKMALIQMG 166

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 48.4 bits (115), Expect = 3e-07
 Identities = 20/115 (17%), Positives = 38/115 (33%), Gaps = 7/115 (6%)

Query: 104 IFVGRL-PQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR--S 160
           + V  L P+  T + L   F  +G +  V +      +    V  A+   A         
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--KKENALVQMADGNQAQLAMSHLNG 63

Query: 161 HEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDW 215
           H++ G+ + I  +   +   P +            YG       +  GS +F + 
Sbjct: 64  HKLHGKPIRITLSKHQNVQLPREG--QEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 104 IFVGRLPQ------EATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADR 155
           I V  +PQ      E     + + FS+FG+I + + P+  G  +G+ F+ +A    A  
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTFAE 149
                + R+G  +FV  L  +   + L+  FS  G ++   + + + G  RG G VTF +
Sbjct: 6   SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQ 65

Query: 150 EVVADR 155
            + A +
Sbjct: 66  SIEAVQ 71

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 7/70 (10%)

Query: 93  RGESSQRIGKKIFVGRLPQ------EATAEDLRRYFSRFGRILDVYVPKRTGH-RGFGFV 145
           R + +  I   I V  +PQ      E     + + FS+FG+I + + P+  G  +G+ F+
Sbjct: 7   RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFL 66

Query: 146 TFAEEVVADR 155
            +A    A  
Sbjct: 67  EYASPAHAVD 76

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 52.3 bits (126), Expect = 2e-09
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 10/92 (10%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGH----RGFGFVTFAEEVVAD 154
              +F+  L    T E L+  FS+ G I    + K+          GFGFV + +   A 
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 155 RVSRR--SHEICGQQVAIDSATPLDD--AGPS 182
           +  ++   H + G ++ +  +       +GPS
Sbjct: 65  KALKQLQGHTVDGHKLEVRISERATKPASGPS 96

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

 Score = 52.1 bits (125), Expect = 3e-09
 Identities = 13/74 (17%), Positives = 21/74 (28%), Gaps = 7/74 (9%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV----S 157
             + +  L       DL      FG I  V V      +    V F + + A       +
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---KKRQALVEFEDVLGACNAVNYAA 78

Query: 158 RRSHEICGQQVAID 171
                I G    ++
Sbjct: 79  DNQIYIAGHPAFVN 92

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

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 14/91 (15%), Positives = 32/91 (35%), Gaps = 7/91 (7%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTG-HRGFGFVT 146
                 +     ++VG      T + L +     G   ++++     +  G  +G+  V 
Sbjct: 46  YTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVV 105

Query: 147 FAEEVVADRVSRR--SHEICGQQVAIDSATP 175
            A E    ++        + G++V +  AT 
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRPATR 136

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 51.5 bits (124), Expect = 5e-09
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH----RGFGFVTFAEEVVADR-V 156
              F+G LP + T E ++ +F     I  V +P+   +    +GFG+  F +       +
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 157 SRRSHEICGQQVAIDSATPLDD 178
           S     +  +++ +D A    D
Sbjct: 79  SLNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 11  RGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKED 49
           +G G+  F   DS+ + L ++   LG   + VD A   +D
Sbjct: 61  KGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQD 100

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 53.6 bits (128), Expect = 5e-09
 Identities = 17/146 (11%), Positives = 38/146 (26%), Gaps = 16/146 (10%)

Query: 8   KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAY 65
           K+  G   +  A   +V+  +  ++ + + G  + V  +            +  G     
Sbjct: 39  KSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYK 98

Query: 66  NAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF 125
           +   S   R++                     Q     +     P E T E+        
Sbjct: 99  DFSESRNNRFSTPEQA-----------AKNRIQHPSNVLHFFNAPLEVTEENFFEICDEL 147

Query: 126 GRILDVYV---PKRTGHRGFGFVTFA 148
           G      V     ++     G + + 
Sbjct: 148 GVKRPTSVKVFSGKSERSSSGLLEWD 173

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 43.2 bits (101), Expect = 2e-05
 Identities = 12/56 (21%), Positives = 18/56 (32%), Gaps = 3/56 (5%)

Query: 101 GKKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
              + V  L Q     + +   F  +G +  V   K     G   V  A+    DR
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDR 57

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 51.0 bits (123), Expect = 6e-09
 Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGH-RGFGFVTFAEEVVADRVSR 158
            IF+G L  E   + L   FS FG IL    +     TG+ +G+ F+ FA    +D    
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 159 RSH--EICGQQVAIDSATPLDDAGPSQN 184
             +   +C + + +  A   D  G   +
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 51.2 bits (123), Expect = 6e-09
 Identities = 18/72 (25%), Positives = 26/72 (36%), Gaps = 11/72 (15%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD----------VYVPKRTGH-RGF 142
              S      IFV  L +  T E +  YF + G I            +Y  + TG  +G 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 143 GFVTFAEEVVAD 154
             V+F +   A 
Sbjct: 66  ATVSFDDPPSAK 77

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 54.1 bits (129), Expect = 6e-09
 Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 4/56 (7%)

Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           I++  L ++   ++L++     FS+FG+ILD+ V +    RG  FV F E   A  
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 41.4 bits (96), Expect = 1e-04
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 105 FVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           F+  LP+E     L   F++F    +V +    G     FV F  EV A  
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRL--VPGRHDIAFVEFDNEVQAGA 259

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 51.1 bits (123), Expect = 6e-09
 Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR 158
           K +FV  L ++ T E L+     F   +   +   + TG  +GFGFV F  E  A     
Sbjct: 16  KTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72

Query: 159 R--SHEICGQQVAIDSATPLDDAGPS 182
                EI G +V +D A P  + G  
Sbjct: 73  AMEDGEIDGNKVTLDWAKPKGEGGSG 98

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          +  D+ + + +G GF+ F S +  +     ++  E+ G+ V +D A PK +
Sbjct: 44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE 94

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

 Score = 52.5 bits (126), Expect = 9e-09
 Identities = 23/107 (21%), Positives = 33/107 (30%), Gaps = 3/107 (2%)

Query: 52  RPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQR-IGKKIFVGRLP 110
           R  G   +    A       A        P  + H     G G       G K+ V  L 
Sbjct: 38  RGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLD 97

Query: 111 QEATAEDLRRYFSRFGRILDVYVPK-RTGH-RGFGFVTFAEEVVADR 155
              +  D++  F+ FG +    V   R+G   G   V F     A +
Sbjct: 98  FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 144

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 50.3 bits (121), Expect = 9e-09
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTGH-RGFGFVTFAEEVVADRVS 157
            +++G L    T EDL       G   IL++     +  G  +GF  V    E  + ++ 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 158 RR--SHEICGQQVAIDSATP 175
                 E+ GQ   +  +  
Sbjct: 63  DLLPKRELHGQNPVVTPSNK 82

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 11 RGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          +G   +   S  S + LM  +   EL G   VV  +   E 
Sbjct: 45 KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH 85

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.7 bits (122), Expect = 9e-09
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGHR--GFGFVTFAEEVVADR-V 156
              F+G LP + T E ++ +F     I  V +P       R  GFG+  F +       +
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 157 SRRSHEICGQQVAIDSATP 175
           S     +  +++ +D A  
Sbjct: 75  SLNEESLGNKRIRVDVADQ 93

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 10/91 (10%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           SS      I V  LPQ++  +++      +  +   YV +   ++   FVT      A  
Sbjct: 2   SSGS--SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR---NKRTAFVTLLNGEQAQN 55

Query: 156 VSRRSH--EICGQQ--VAIDSATPLDDAGPS 182
             +  H     G+   V +     L  +GPS
Sbjct: 56  AIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 88  GSFYGRGE-SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVT 146
           GS    G    ++  +K+ +  +P     E L     ++G +                VT
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60

Query: 147 FAEEVVADR 155
           ++ +  A +
Sbjct: 61  YSSKDQARQ 69

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 50.7 bits (121), Expect = 1e-08
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 7/88 (7%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
           GS  G   S+    + I + +LP + T  ++      FG++ ++ + K    +   F+  
Sbjct: 18  GSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK---GKNQAFIEM 74

Query: 148 AEEVVADRVSRRSH----EICGQQVAID 171
             E  A+ +          + GQ + I 
Sbjct: 75  NTEEAANTMVNYYTSVTPVLRGQPIYIQ 102

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

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 23/106 (21%), Positives = 33/106 (31%), Gaps = 13/106 (12%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILD----------VYVPKRTGH-RGFGFVTFAEE 150
             IFV  L +  T E +  YF + G I            +Y  + TG  +G   V+F + 
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 151 VVADRVSRR--SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFG 194
             A          E  G  + +  AT   D            E   
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHH 113

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +  D+ +   +G   ++F    S +      D  E  G+ + V  AT +  DF   G   
Sbjct: 47  LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA-DFNRGGGNG 105

Query: 59  HGGYGAYNAY 68
            GG   ++ +
Sbjct: 106 RGGLEHHHHH 115

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 49.0 bits (117), Expect = 3e-08
 Identities = 15/74 (20%), Positives = 22/74 (29%), Gaps = 7/74 (9%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA----DRVS 157
             + V  L +     DL     +FG I  V +      +    V F     A       +
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAA 72

Query: 158 RRSHEICGQQVAID 171
                I GQQ   +
Sbjct: 73  DVPVYIAGQQAFFN 86

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 49.1 bits (117), Expect = 4e-08
 Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVAD 154
                +   ++VG LP++A   DL+R     G +      +  G R   F+ + +   A 
Sbjct: 13  GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ--GPRRRAFLHYPDSAAAQ 70

Query: 155 RV--SRRSHEICGQQVAIDSATP 175
           +     +   +    + +  A  
Sbjct: 71  QAVSCLQGLRLGTDTLRVALARQ 93

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

 Score = 51.2 bits (122), Expect = 4e-08
 Identities = 18/148 (12%), Positives = 41/148 (27%), Gaps = 16/148 (10%)

Query: 8   KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAY 65
              +    +  A  +  +  M  ++ H+L G  + +  +  +       G+   G    Y
Sbjct: 69  FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDY 128

Query: 66  NAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF 125
                   +            P                + +  +P   + EDL+  FS  
Sbjct: 129 GNSPLHRFKKPGSKNFQNIFPPS-------------ATLHLSNIPPSVSEEDLKVLFSSN 175

Query: 126 GRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           G ++  +   +   R    +       A
Sbjct: 176 GGVVKGFKFFQKD-RKMALIQMGSVEEA 202

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

 Score = 45.8 bits (108), Expect = 3e-06
 Identities = 19/119 (15%), Positives = 38/119 (31%), Gaps = 8/119 (6%)

Query: 72  ATRYAALGAPTLYDHPGSFYGRGE---SSQRIGKKIFVGRL-PQEATAEDLRRYFSRFGR 127
            + +      +     GS  GR      +      + V  L P+  T + L   F  +G 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 128 ILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR--SHEICGQQVAIDSATPLDDAGPSQN 184
           +  V +      +    V  A+   A         H++ G+ + I  +   +   P + 
Sbjct: 62  VQRVKILFN--KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREG 118

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 51.3 bits (122), Expect = 4e-08
 Identities = 22/132 (16%), Positives = 38/132 (28%), Gaps = 8/132 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTGH-RGFGFVTFAEEVVADRVS 157
            +++G L    T EDL       G   IL++     +  G  +GF  V    E  + ++ 
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 158 RR--SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDW 215
                 E+ GQ   +            +       ++    G              F   
Sbjct: 130 DLLPKRELHGQNPVVTPVNK-QFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQG 188

Query: 216 GYGMGSGRPSRG 227
           G G G    +  
Sbjct: 189 GRGRGRFPGAVP 200

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 49.8 bits (119), Expect = 4e-08
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRI--------LDVYVPKRTGHRGFGFVTFAEEVV 152
             +I+V  L +    +DL+  F R+            D+ + K    +G  F+    E  
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 153 ADR 155
           A +
Sbjct: 105 AAK 107

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

 Score = 48.8 bits (117), Expect = 4e-08
 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 5/78 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAEEVVADR-VS 157
              +VG LP      D+   F     I  V +   K T   +GF +V F E       ++
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 158 RRSHEICGQQVAIDSATP 175
                +  + + +D A  
Sbjct: 75  YDGALLGDRSLRVDIAEG 92

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 49.8 bits (119), Expect = 5e-08
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 89  SFYGRGESSQRI---GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGF 142
            F G  E  +++      ++VG L    T E +   FS+ G I  + +   K      GF
Sbjct: 24  HFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF 83

Query: 143 GFVTFAEEVVADRVSRRSH--EICGQQVAIDSATP 175
            FV +     A+   R  +   +  + +  D    
Sbjct: 84  CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 118

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 51.4 bits (122), Expect = 6e-08
 Identities = 25/136 (18%), Positives = 40/136 (29%), Gaps = 3/136 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR 158
           K +FV R+  + T   LRR F  +G I  +++   KR+G  RG+ F+ +  E       +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 159 RSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRTYGRMYGSLDFDDWGYG 218
            +         +                       G   G      R  G  D   +   
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDER 222

Query: 219 MGSGRPSRGDWRYRPY 234
            G       D      
Sbjct: 223 PGPSPLPHRDRDRDRE 238

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 48.6 bits (116), Expect = 6e-08
 Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 11/74 (14%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD----------VYVPKRTGH-R 140
                       I+V  L    T +DL  +F + G +            +Y+ K TG  +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

Query: 141 GFGFVTFAEEVVAD 154
           G   V++ +   A 
Sbjct: 66  GDATVSYEDPPTAK 79

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

 Score = 48.3 bits (115), Expect = 7e-08
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 7/92 (7%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
           GS +     S    + I + +LP + T  ++      FG++ ++ + K    +   F+  
Sbjct: 3   GSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK---GKNQAFIEM 59

Query: 148 AEEVVADRVSRRSH----EICGQQVAIDSATP 175
             E  A+ +          + GQ + I  +  
Sbjct: 60  NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.4 bits (117), Expect = 1e-07
 Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 3/93 (3%)

Query: 84  YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTGHRG 141
              P         +    + +++   P +AT +D++ +    G++L++ + +      +G
Sbjct: 92  PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 151

Query: 142 FGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 173
             FV F     A + V     +     + I   
Sbjct: 152 SIFVVFDSIESAKKFVETPGQKYKETDLLILFK 184

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 47.5 bits (113), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV---- 156
            + + + +LP E T  ++      FG++ ++ + K    +   F+  A E  A  +    
Sbjct: 15  SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYY 71

Query: 157 SRRSHEICGQQVAIDSAT 174
           S  +  +  Q + I  + 
Sbjct: 72  SAVTPHLRNQPIYIQYSN 89

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 19/93 (20%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTG-HRGFG 143
            G    R  S    G  +++  LP EA  + +  +F +   + D         G   G G
Sbjct: 11  SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70

Query: 144 FVTFAEEVVADR-VSRRSHEICGQQVAIDSATP 175
           FV F  E      + R    +  + + +   T 
Sbjct: 71  FVEFRNEADYKAALCRHKQYMGNRFIQVHPITK 103

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGHRGFGFVTFAEEVVADRVSRRS 160
           + +  LP   + E++ ++FS    + +   + V  +    G  FV FA + +A++  ++ 
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77

Query: 161 HEICGQ---QVAIDSATPLDDAGPS 182
            E  G    ++   S   +  +GPS
Sbjct: 78  KERIGHRYIEIFKSSRAEVRTSGPS 102

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 3/59 (5%)

Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR 155
           +     +         + L   FS+ G+++++  P  + TG  +GF FV       A +
Sbjct: 11  VNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKK 69

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 45.0 bits (107), Expect = 9e-07
 Identities = 21/101 (20%), Positives = 38/101 (37%), Gaps = 19/101 (18%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGH-RGFGFVTFAEEV 151
            S  +   +++G L        + R F+  G  +    +   + TG   G+ FV FA+  
Sbjct: 4   GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 152 VADRVSRRSHEICGQQVAIDS--ATPLDDAGPSQNFMMNAA 190
            A++              +      PL  A P++ F +N A
Sbjct: 64  TAEK-------------CLHKINGKPLPGATPAKRFKLNYA 91

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 45.6 bits (108), Expect = 9e-07
 Identities = 19/109 (17%), Positives = 41/109 (37%), Gaps = 6/109 (5%)

Query: 73  TRYAALGAPTLYDHPGSFYGRGESSQRI--GKKIFVGRLPQEATAEDLRRYFSRFGRILD 130
           +     G+       G   GRG +S        + +  LP   T E++ ++FS    + +
Sbjct: 12  SGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPN 71

Query: 131 VYVP---KRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSATP 175
                        G  FV FA + +A++ + +    I  + + +  ++ 
Sbjct: 72  GITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQ 120

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFS-RFGRILDVYVPK-RTGH-RGFGFVTFAEEVVADR 155
           +FVG L  +     L  +F   +       V   +TG  +G+GFV F +E+   R
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKR 66

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 4/79 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPK-RTG-HRGFGFVTFAEEVVADRVS 157
                +  +P   T  D+ ++        + V+V     G   G   V F  E  A +  
Sbjct: 15  KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74

Query: 158 RRSHE-ICGQQVAIDSATP 175
           R   + + G++  +   T 
Sbjct: 75  RLHRKKLNGREAFVHVVTL 93

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 9/73 (12%), Positives = 25/73 (34%), Gaps = 8/73 (10%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH-- 161
           +  G L    +   L     + G +  + +P    ++ + F  +     + R     +  
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGK 86

Query: 162 ---EICGQQVAID 171
              +  GQ++ + 
Sbjct: 87  EVVDDLGQKITLY 99

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFAEEVVADRVSR 158
           G  + +  LP  AT  D+  +FS     + V++         G   V FA    A     
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA 73

Query: 159 RSHEICGQ---QVAIDSATPLDDAGPS 182
           +          ++ ++S      +GPS
Sbjct: 74  KDKANMQHRYVELFLNSTAGTSGSGPS 100

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 42.8 bits (101), Expect = 5e-06
 Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 8/65 (12%)

Query: 99  RIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVPKRTGHRGFGFVTFAEE 150
              ++++VG +P   T E +  +F+   R+          V   +    + F F+ F   
Sbjct: 4   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63

Query: 151 VVADR 155
               +
Sbjct: 64  DETTQ 68

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 43.2 bits (102), Expect = 5e-06
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
            S    G  S+R   ++ V  LP   + +DL+ +    G +    V +     G G V F
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEF 57

Query: 148 AEEVVADR 155
             +     
Sbjct: 58  VRKEDMTY 65

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 42.3 bits (100), Expect = 7e-06
 Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHR--GFGFVTFAE 149
           G   SS      + +   P   T +++  + +     + + + +       G+ FV F+ 
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 150 E 150
           E
Sbjct: 60  E 60

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 15/105 (14%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD----VYVPK--RTGHRGFGFVTFAEEVVADRVS 157
           + +  LP  ATAE++  +F +   I      +           G  FV FA E  A    
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 158 RRSHE-ICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMR 201
           R+  + +  + + +  +T  +        +      F    GP  
Sbjct: 86  RKHKDLLGKRYIELFRSTAAE--------VQQVLNRFSSASGPSS 122

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 18/117 (15%), Positives = 38/117 (32%), Gaps = 6/117 (5%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTF 147
                 G  S+R   ++ V  LP   + +DL+ +    G +    V +     G G V F
Sbjct: 3   APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEF 58

Query: 148 AEEVVADRVSRR--SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRT 202
             +       R+  + +    +          D   S ++  + + +        R+
Sbjct: 59  VRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRSRS 115

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG--HRGFGFVTFAE 149
           G+          + V  +P  A   D+R +F    R+  V++ K     + G G V F  
Sbjct: 7   GKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLS 65

Query: 150 EVVADR-VSRRSHEICGQQVAIDSATP 175
                  + R    +  + V +  AT 
Sbjct: 66  PQDTFEALKRNRMLMIQRYVEVSPATE 92

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 15/93 (16%), Positives = 27/93 (29%), Gaps = 5/93 (5%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGF 144
            S      S +     I V  +P   + +++  +F  +  I      K    G   G   
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 145 VTFAEEVVADRV--SRRSHEICGQQVAIDSATP 175
           V F     A           I  ++V +   + 
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 3/71 (4%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TG-HRGFGF 144
            S      S +     I V  +P   + +++  +F  +  I      K    G   G   
Sbjct: 2   SSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 145 VTFAEEVVADR 155
           V F     A  
Sbjct: 62  VAFESRDEATA 72

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

 Score = 42.5 bits (99), Expect = 4e-05
 Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 13/86 (15%)

Query: 79  GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATA---------EDLRRYFSRFGRIL 129
           G     D+     G G S ++  K ++VG +     +           +R  FSR G I 
Sbjct: 113 GREKFADYREDMGGIG-SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDID 171

Query: 130 DVYVPKRTGHRGFGFVTFAEEVVADR 155
            +   +    +  GFV F  +  A+ 
Sbjct: 172 RIRYVES---KNCGFVKFKYQANAEF 194

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 17/101 (16%), Positives = 27/101 (26%), Gaps = 9/101 (8%)

Query: 74  RYAALGAPTLYDHPGSFYGRGESSQRIGKK----IFVGRLPQEATAEDLRRYFSRF---G 126
                G+       G   GRG             + +  LP   + ED++ + S      
Sbjct: 13  GLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHD 72

Query: 127 RILDVYVPK--RTGHRGFGFVTFAEEVVADRVSRRSHEICG 165
               V+          G  FV    E       ++  E  G
Sbjct: 73  GAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMG 113

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 19/90 (21%), Positives = 28/90 (31%), Gaps = 9/90 (10%)

Query: 74  RYAALGAPTLYDHPGSFYGRGESSQRI------GKKIFVGRLPQEATAEDLRRYFSRFGR 127
                G+       G   GRG            G  + +  LP +AT  D+  +FS    
Sbjct: 13  GLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN- 71

Query: 128 ILDVYVPKRTG--HRGFGFVTFAEEVVADR 155
            + V++         G   V FA    A  
Sbjct: 72  PVRVHIEIGPDGRVTGEADVEFATHEEAVA 101

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 93  RGESSQRIGKKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEV 151
           + +  Q +G+ I +  LP    +   + +    +G+I +  + +    +   F+      
Sbjct: 17  KFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETRE 73

Query: 152 VADRVSRRSHE----ICGQQVAID 171
            A  +     +      G+ V +D
Sbjct: 74  DAMAMVDHCLKKALWFQGRCVKVD 97

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 8/81 (9%)

Query: 94  GESSQRIGKKIFVGR---LPQEATAEDLRRYFSRF---GRILDVYVPKRTGHR--GFGFV 145
           G   +     +F+ R   LP   T ED+  +FS          ++       +  G   +
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60

Query: 146 TFAEEVVADRVSRRSHEICGQ 166
               E    +   +     GQ
Sbjct: 61  EMESEQDVQKALEKHRMYMGQ 81

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 14/99 (14%), Positives = 32/99 (32%), Gaps = 9/99 (9%)

Query: 85  DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF---GRILDVYVPKRTGHR- 140
              G   G       +   + +  LP   + ED++ + S       +  V+       R 
Sbjct: 4   GSSGMMLGPEGGEGYV---VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60

Query: 141 -GFGFVTFA-EEVVADRVSRRSHEICGQQVAIDSATPLD 177
            G  FV    E+ V   + +    +  + + +  +   +
Sbjct: 61  SGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTE 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 12/75 (16%), Positives = 23/75 (30%), Gaps = 3/75 (4%)

Query: 84  YDHPGSFYGRGESSQRIGK---KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHR 140
           + H      RG    ++     +I +  LP+  + +DL+                     
Sbjct: 8   HHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFD 67

Query: 141 GFGFVTFAEEVVADR 155
           G G + F  E +   
Sbjct: 68  GTGALEFPSEEILVE 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	234
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.95
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.95
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.94
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.94
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.93
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.93
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.93
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.92
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.92
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.91
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.91
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.91
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.89
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.89
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.89
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.84
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.84
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.83
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.83
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.83
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.83
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.83
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.83
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.83
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.83
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.83
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.82
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.82
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.82
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.82
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.82
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.82
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.82
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.82
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.82
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.82
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.82
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.82
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.81
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.8
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.8
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.8
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.8
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.8
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.8
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.8
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.8
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.79
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.79
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.79
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.79
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.79
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.79
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.79
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.79
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.79
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.78
2div_A	99	TRNA selenocysteine associated protein; structural	99.78
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.78
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.78
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.78
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.78
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.78
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.78
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.77
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.77
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.77
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.77
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.77
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.77
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.77
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.77
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.76
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.76
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.76
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.76
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.75
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.75
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.75
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.75
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
1x5p_A	97	Negative elongation factor E; structure genomics,	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.74
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.74
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.6
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.74
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.74
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.74
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.73
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.73
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.72
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.71
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.7
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.69
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.69
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.68
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.68
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.67
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.67
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.67
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.66
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.65
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.62
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.61
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.6
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.6
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.58
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.58
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.56
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.54
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.54
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.53
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.52
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.47
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.45
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.43
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.42
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.39
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.33
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.32
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.27
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.25
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.2
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.2
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.14
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.12
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.1
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.1
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.1
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.05
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.04
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.03
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.03
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.03
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.03
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.03
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.03
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.03
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.03
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.03
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.03
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.02
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.02
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.02
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.02
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.01
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.01
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.01
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.01
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.0
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.0
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.0
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.0
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.0
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.99
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.99
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.98
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.97
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.97
2div_A	99	TRNA selenocysteine associated protein; structural	98.96
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.96
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.95
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.95
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.94
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.94
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.94
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.93
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.93
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.93
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.93
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.93
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.93
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.92
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.92
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.92
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.91
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.91
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.91
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.9
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.9
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.9
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.9
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.9
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.89
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.41
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.88
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.88
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.87
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.87
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.86
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.86
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.86
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.85
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.85
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.84
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.83
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.83
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.82
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.82
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.81
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.81
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.78
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.77
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.77
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.77
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.76
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.76
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.73
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.72
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.71
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.7
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.69
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.69
1x5p_A	97	Negative elongation factor E; structure genomics,	98.67
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.67
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.66
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.62
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.62
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.62
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.6
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.6
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.59
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.58
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.58
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.57
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.55
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.54
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.54
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.52
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.52
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.51
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.5
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.5
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.49
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.49
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.47
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.46
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.46
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.45
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.44
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.44
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.43
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.43
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.43
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.42
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.42
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.42
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.41
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.4
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.39
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.38
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.3
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.28
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.15
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.14
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.93
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.7
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.66
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.55
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	97.3
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.3
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.3
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	97.17
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.88
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.82
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.56
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.56
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.5
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.41
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.31
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	94.88
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	94.32
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	89.65
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	84.28

>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=99.97  E-value=4.4e-30  Score=198.99  Aligned_cols=139  Identities=31%  Similarity=0.597  Sum_probs=111.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      |++|+.|++++|||||+|.+.++|++||. +++.|.|+.|.|.++.++.....+.                         
T Consensus        45 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~~~~~~~-------------------------   99 (196)
T 1l3k_A           45 VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG-------------------------   99 (196)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC---------------------------------
T ss_pred             EEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCcccccccc-------------------------
Confidence            46788999999999999999999999995 6789999999999987654322110                         


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                       .....++|||+|||+++|+++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|.+|
T Consensus       100 -----------------~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A  162 (196)
T 1l3k_A          100 -----------------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  162 (196)
T ss_dssp             --------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH
T ss_pred             -----------------cCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHH
Confidence                             13456899999999999999999999999999999998  3466 899999999999999999


Q ss_pred             Hh-cCCccCCeEeEEEeCCCCCCCCC
Q 026724          157 SR-RSHEICGQQVAIDSATPLDDAGP  181 (234)
Q Consensus       157 ~~-~~~~~~g~~i~v~~a~~~~~~~~  181 (234)
                      |. +++.|+|+.|.|.++.++.+...
T Consensus       163 ~~~~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          163 VIQKYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHCSCCEETTEECEEEECC-------
T ss_pred             HHhCCcEECCEEEEEEecCChhHhcc
Confidence            84 67799999999999999887654

>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=99.96  E-value=6.4e-30  Score=193.20  Aligned_cols=129  Identities=33%  Similarity=0.627  Sum_probs=114.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGA   80 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (234)
                      |++|+.|++++|||||+|.+.++|++||.+++.|+|+.|.|.++.++..                               
T Consensus        35 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~-------------------------------   83 (167)
T 2cjk_A           35 IMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE-------------------------------   83 (167)
T ss_dssp             CCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHH-------------------------------
T ss_pred             EEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhh-------------------------------
Confidence            5789999999999999999999999999988999999999988764321                               


Q ss_pred             CCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH
Q 026724           81 PTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~  157 (234)
                                       .....+|||+|||+++++++|+++|++||.|..|.++  +.++ ++|||||+|.+.++|.+|+
T Consensus        84 -----------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~  146 (167)
T 2cjk_A           84 -----------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC  146 (167)
T ss_dssp             -----------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHH
T ss_pred             -----------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHH
Confidence                             1135689999999999999999999999999999998  3467 9999999999999999999


Q ss_pred             h-cCCccCCeEeEEEeCCCCC
Q 026724          158 R-RSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       158 ~-~~~~~~g~~i~v~~a~~~~  177 (234)
                      . ++..+.|+.|.|.+|.|+.
T Consensus       147 ~~~~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          147 QNKFIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             HCSEECSSSSCEEEEECCCCC
T ss_pred             hCCCEEeCCeEEEEeecCCCC
Confidence            5 6679999999999999864

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=4.3e-29  Score=196.41  Aligned_cols=132  Identities=19%  Similarity=0.290  Sum_probs=115.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|++++|||||+|.+.++|++||.  ++..+.|+.|+|.++.......                           
T Consensus        47 i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~---------------------------   99 (213)
T 4f02_A           47 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR---------------------------   99 (213)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHH---------------------------
T ss_pred             EecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccccccccc---------------------------
Confidence            46899999999999999999999999994  6889999999999876432211                           


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~  157 (234)
                                         .....+|||+|||+++|+++|+++|++||.|..|.|+.+.+ ++|||||+|.+.++|.+||
T Consensus       100 -------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai  160 (213)
T 4f02_A          100 -------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI  160 (213)
T ss_dssp             -------------------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHH
T ss_pred             -------------------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHH
Confidence                               12356899999999999999999999999999999995555 8999999999999999998


Q ss_pred             --hcCCccCCeEeEEEeCCCCCC
Q 026724          158 --RRSHEICGQQVAIDSATPLDD  178 (234)
Q Consensus       158 --~~~~~~~g~~i~v~~a~~~~~  178 (234)
                        +++..|+|+.|+|.+|.++.+
T Consensus       161 ~~lng~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          161 EKMNGMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             HHHTTCEETTEECEEEECCCHHH
T ss_pred             HHhCCCEECCEEEEEEEcCCCcc
Confidence              478899999999999988654

>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=99.95  E-value=3.9e-28  Score=184.90  Aligned_cols=128  Identities=19%  Similarity=0.346  Sum_probs=111.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      +++|..++++||||||+|.+.++|++||+ +++.|.|++|.|.++.++....                            
T Consensus        44 ~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~~~----------------------------   95 (175)
T 1fje_B           44 AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKK----------------------------   95 (175)
T ss_dssp             CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSSCST----------------------------
T ss_pred             EEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCccccc----------------------------
Confidence            36778899999999999999999999994 7889999999999987653221                            


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~  158 (234)
                                        ....++|||+|||+++++++|+++|++||.|..+   ..++ ++|||||+|.+.++|.+|+.
T Consensus        96 ------------------~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~A~~A~~  154 (175)
T 1fje_B           96 ------------------VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLE  154 (175)
T ss_dssp             ------------------TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE---CSSSSCCSEEEEECSSHHHHHHHHH
T ss_pred             ------------------cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe---cCCCCCceEEEEEECCHHHHHHHHH
Confidence                              2346799999999999999999999999998776   5555 89999999999999999984


Q ss_pred             --cCCccCCeEeEEEeCCCCC
Q 026724          159 --RSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       159 --~~~~~~g~~i~v~~a~~~~  177 (234)
                        ++..|.|+.|.|.++.++.
T Consensus       155 ~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          155 EKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             HHTEEEETTEEEEEEECSSCC
T ss_pred             HhCCCEECCeEEEEEecCCCC
Confidence              7789999999999998863

>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=99.95  E-value=2.9e-27  Score=178.63  Aligned_cols=125  Identities=21%  Similarity=0.351  Sum_probs=110.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|++++|||||+|.+.++|++|+.  ++..|.|++|.|.++.+...                             
T Consensus        35 i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-----------------------------   85 (168)
T 1b7f_A           35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE-----------------------------   85 (168)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS-----------------------------
T ss_pred             EEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc-----------------------------
Confidence            46788899999999999999999999994  78899999999999875432                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~  155 (234)
                                         ....++|||+|||..+++++|+++|++||.|..+.++.  .++ ++|||||+|.+.++|.+
T Consensus        86 -------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~  146 (168)
T 1b7f_A           86 -------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE  146 (168)
T ss_dssp             -------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             -------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHH
Confidence                               23467999999999999999999999999999999883  356 89999999999999999


Q ss_pred             HH--hcCCccCC--eEeEEEeC
Q 026724          156 VS--RRSHEICG--QQVAIDSA  173 (234)
Q Consensus       156 A~--~~~~~~~g--~~i~v~~a  173 (234)
                      |+  +++..+.|  ++|+|++|
T Consensus       147 A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          147 AISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCEecCCCeEEEEEeC
Confidence            98  47788987  99999986

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.95  E-value=6e-27  Score=176.34  Aligned_cols=127  Identities=21%  Similarity=0.353  Sum_probs=110.3

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      ++|+. ++++|||||+|.+.++|++|+.  ++..|.|+.|.|.++.+.....                            
T Consensus        33 ~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~~----------------------------   83 (166)
T 3md3_A           33 MIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSS----------------------------   83 (166)
T ss_dssp             ECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCCCC----------------------------
T ss_pred             EECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCCC----------------------------
Confidence            45664 7799999999999999999994  7889999999999986543211                            


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                        .....+|||+|||+.+++++|+++|++||.|..+.++  +.++ ++|||||+|.+.++|.+|
T Consensus        84 ------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A  145 (166)
T 3md3_A           84 ------------------SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA  145 (166)
T ss_dssp             ------------------CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             ------------------CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHH
Confidence                              3457799999999999999999999999999999998  4566 899999999999999999


Q ss_pred             H--hcCCccCCeEeEEEeCCC
Q 026724          157 S--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       157 ~--~~~~~~~g~~i~v~~a~~  175 (234)
                      +  +++..++|+.|+|.||++
T Consensus       146 ~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          146 MDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHTTCEETTEECEEEESCC
T ss_pred             HHHhCCCccCCcEEEEEecCC
Confidence            8  478899999999999864

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

Probab=99.95  E-value=4.1e-27  Score=184.92  Aligned_cols=143  Identities=20%  Similarity=0.407  Sum_probs=114.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|++++|||||+|.+.++|++||+  ++..|.|+.|.|.++........                  ....... 
T Consensus        60 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~------------------~~~~~~~-  120 (216)
T 2qfj_A           60 MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP------------------IIDQLAE-  120 (216)
T ss_dssp             ECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHH------------------HHHHHHH-
T ss_pred             EeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccch------------------hhhhhhc-
Confidence            46888899999999999999999999995  68899999999988764432100                  0000000 


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~  155 (234)
                                        .....++|||+|||.++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|.+
T Consensus       121 ------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~  182 (216)
T 2qfj_A          121 ------------------EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD  182 (216)
T ss_dssp             ------------------HHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             ------------------ccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHH
Confidence                              02346899999999999999999999999999999998  3466 89999999999999999


Q ss_pred             HHh--cCCccCCeEeEEEeCCCCCCCC
Q 026724          156 VSR--RSHEICGQQVAIDSATPLDDAG  180 (234)
Q Consensus       156 A~~--~~~~~~g~~i~v~~a~~~~~~~  180 (234)
                      |+.  ++..|.|+.|+|.++.++....
T Consensus       183 A~~~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          183 AVSSMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             HHHHHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             HHHHccCCEeCCcEEEEEEecCCCCCC
Confidence            984  7889999999999999876544

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=1e-26  Score=180.19  Aligned_cols=148  Identities=18%  Similarity=0.302  Sum_probs=115.6

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPT   82 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (234)
                      +..+++++|||||+|.+.++|++|| ++++.|.|++|.|.++...............                       
T Consensus        44 ~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~-----------------------  100 (198)
T 2yh0_A           44 AVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSV-----------------------  100 (198)
T ss_dssp             EEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEECCCCCCCCCCSSSCSSC-----------------------
T ss_pred             EeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEeCCCCCCCCCCCcCCCcC-----------------------
Confidence            3456789999999999999999999 4688999999999988765432211000000                       


Q ss_pred             ccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CCC-CcceEEEEEcChHHHHHHHh-
Q 026724           83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSR-  158 (234)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~A~~-  158 (234)
                        ..+.   ..........++|||+|||+.+++++|+++|++||.|..|.++.  .++ ++|||||+|.+.++|.+|+. 
T Consensus       101 --~~~~---~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~  175 (198)
T 2yh0_A          101 --YVPG---VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  175 (198)
T ss_dssp             --CCTT---SSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHH
T ss_pred             --CCCC---CccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHH
Confidence              0000   00111135678999999999999999999999999999999983  366 89999999999999999984 


Q ss_pred             -cCCccCCeEeEEEeCCCCCCC
Q 026724          159 -RSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       159 -~~~~~~g~~i~v~~a~~~~~~  179 (234)
                       ++..|+|+.|.|.++.++...
T Consensus       176 l~g~~~~g~~l~v~~a~~~~~~  197 (198)
T 2yh0_A          176 LNGMQLGDKKLLVQRASVGAKN  197 (198)
T ss_dssp             HTTCEETTEECEEEESCCCCCC
T ss_pred             cCCCEECCEEEEEEECCCCCCC
Confidence             788999999999999987643

>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=99.95  E-value=6.9e-27  Score=176.18  Aligned_cols=125  Identities=24%  Similarity=0.488  Sum_probs=109.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.|++++|||||+|.+.++|++|++  ++..|.|++|.|.++.+...                             
T Consensus        34 ~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-----------------------------   84 (167)
T 1fxl_A           34 LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA-----------------------------   84 (167)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG-----------------------------
T ss_pred             EEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc-----------------------------
Confidence            35788899999999999999999999994  78899999999999875432                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~  155 (234)
                                         .....+|||+|||..+++++|+++|++||.|..+.++  +.++ ++|||||+|.+.++|.+
T Consensus        85 -------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~  145 (167)
T 1fxl_A           85 -------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE  145 (167)
T ss_dssp             -------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             -------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHH
Confidence                               2246789999999999999999999999999999988  3356 89999999999999999


Q ss_pred             HHh--cCCccCCeE--eEEEeC
Q 026724          156 VSR--RSHEICGQQ--VAIDSA  173 (234)
Q Consensus       156 A~~--~~~~~~g~~--i~v~~a  173 (234)
                      |+.  ++..+.|+.  |.|+||
T Consensus       146 A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          146 AIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCccCCCccceEEEeC
Confidence            984  788999975  888876

>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=99.94  E-value=1.2e-26  Score=175.98  Aligned_cols=122  Identities=19%  Similarity=0.405  Sum_probs=106.6

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCc
Q 026724            5 QGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTL   83 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (234)
                      ..++++||||||+|.+.++|++|+ ++++.|.|++|.|.++.....                                  
T Consensus        45 ~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~~----------------------------------   90 (172)
T 2g4b_A           45 VQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQP----------------------------------   90 (172)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEECEEECCSSCCC----------------------------------
T ss_pred             eEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceeeecCCcccCC----------------------------------
Confidence            345788999999999999999999 468899999999998654321                                  


Q ss_pred             cCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CCC-CcceEEEEEcChHHHHHHHh--
Q 026724           84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSR--  158 (234)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~A~~--  158 (234)
                                    .....+|||+|||+.+++++|+++|++||.|..|.++.  .++ ++|||||+|.+.++|.+|+.  
T Consensus        91 --------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           91 --------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             --------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             --------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence                          22367899999999999999999999999999999983  466 89999999999999999984  


Q ss_pred             cCCccCCeEeEEEeCC
Q 026724          159 RSHEICGQQVAIDSAT  174 (234)
Q Consensus       159 ~~~~~~g~~i~v~~a~  174 (234)
                      ++..++|+.|.|++|.
T Consensus       157 ~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTCEETTEECEEEECC
T ss_pred             CCCEECCeEEEEEeCC
Confidence            7889999999999973

>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=99.94  E-value=7e-26  Score=185.34  Aligned_cols=134  Identities=16%  Similarity=0.229  Sum_probs=117.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+.||+++|||||+|.+.++|.+|+.  ++..|.|++|.|.++.++.....                          
T Consensus       127 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~--------------------------  180 (284)
T 3smz_A          127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA--------------------------  180 (284)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCTT--------------------------
T ss_pred             EEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcc--------------------------
Confidence            35788899999999999999999999993  78899999999999876532211                          


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCC-CHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADR  155 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~-~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~  155 (234)
                                         ....++|||+|||+.+ ++++|+++|++||.|..|.|+ ..++ ++|+|||+|.+.++|.+
T Consensus       181 -------------------~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~  241 (284)
T 3smz_A          181 -------------------LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEE  241 (284)
T ss_dssp             -------------------TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHH
T ss_pred             -------------------cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHH
Confidence                               3457899999999995 999999999999999999988 4456 89999999999999999


Q ss_pred             HH--hcCCccCCeEeEEEeCCCCCCC
Q 026724          156 VS--RRSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       156 A~--~~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      |+  +++..|.|+.|.|.++.++..+
T Consensus       242 A~~~l~g~~~~g~~l~v~~a~~~~~~  267 (284)
T 3smz_A          242 AQQQADGLSLGGSHLRVSFCAPGPPG  267 (284)
T ss_dssp             HHHHHTTCEETTEECEEEECCSSSCH
T ss_pred             HHHHhCCCccCCeEEEEEEecCCCcc
Confidence            98  4788999999999999987753

>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=99.93  E-value=1.3e-25  Score=168.45  Aligned_cols=83  Identities=27%  Similarity=0.444  Sum_probs=74.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      .....+|||+|||+++++++|+++|++||.|..|.|+.  .++ ++|||||+|.+.++|++||.  +++.|.|+.|+|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999983  467 99999999999999999994  77899999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +.++.+..
T Consensus       147 a~~~~~~~  154 (158)
T 2kn4_A          147 ARYGRPPD  154 (158)
T ss_dssp             ECCSSCCC
T ss_pred             CCCCCCCC
Confidence            99876544

>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=99.93  E-value=2.5e-25  Score=182.69  Aligned_cols=135  Identities=20%  Similarity=0.343  Sum_probs=106.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (234)
                      |++|+. ++++|||||+|.+.++|++|+.  +++.|.|++|.|.++.++......                         
T Consensus       150 i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~-------------------------  203 (292)
T 2ghp_A          150 LPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT-------------------------  203 (292)
T ss_dssp             CC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-------------------------------
T ss_pred             EEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc-------------------------
Confidence            455665 8899999999999999999995  788999999999999865443211                         


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEeec-C--CC-CcceEEEEEcChHHH
Q 026724           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPK-R--TG-HRGFGFVTFAEEVVA  153 (234)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~-~--~~-~~g~afV~f~~~~~a  153 (234)
                                      .......++|||+|||+. +++++|+++|++||.|..|.|+. .  ++ ++|||||+|.+.++|
T Consensus       204 ----------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A  267 (292)
T 2ghp_A          204 ----------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA  267 (292)
T ss_dssp             -------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHH
T ss_pred             ----------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHH
Confidence                            001446789999999999 99999999999999999999983 2  37 899999999999999


Q ss_pred             HHHH-hcCCccCCeEeEEEeCCCCC
Q 026724          154 DRVS-RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       154 ~~A~-~~~~~~~g~~i~v~~a~~~~  177 (234)
                      .+|+ +++..|.|+.|.|.|+.+++
T Consensus       268 ~~A~~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          268 ERALQMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             HHHGGGTTEEETTEEEEEEECCCCC
T ss_pred             HHHHHhcCCEECCcEEEEEEecCCC
Confidence            9999 46779999999999999874

>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=99.93  E-value=1.5e-25  Score=170.26  Aligned_cols=127  Identities=20%  Similarity=0.399  Sum_probs=103.9

Q ss_pred             CCCCCCCC--CccceEEEEEcCHHHHHHHHh--cCceeC---CcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhh
Q 026724            1 MPKDQGSK--AHRGIGFITFASADSVENLMV--DTHELG---GSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAAT   73 (234)
Q Consensus         1 l~rD~~tg--~srG~aFV~F~~~e~A~~Al~--~~~~i~---gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (234)
                      |++|+.++  +++|||||+|.+.++|++|+.  ++..+.   ++.+.+.++.+....                       
T Consensus        35 i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------------------   91 (175)
T 3nmr_A           35 VLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNN-----------------------   91 (175)
T ss_dssp             EEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCS-----------------------
T ss_pred             EEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccc-----------------------
Confidence            35677777  999999999999999999994  555554   577777776543321                       


Q ss_pred             hhhhcCCCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChH
Q 026724           74 RYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEV  151 (234)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~  151 (234)
                                              ....++|||+|||+++|+++|+++|++||.|..|.++ ..++ ++|||||+|.+.+
T Consensus        92 ------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~  147 (175)
T 3nmr_A           92 ------------------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRA  147 (175)
T ss_dssp             ------------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHH
T ss_pred             ------------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHH
Confidence                                    2346789999999999999999999999999999998 4456 8999999999999


Q ss_pred             HHHHHHh--cCCccC---CeEeEEEeCC
Q 026724          152 VADRVSR--RSHEIC---GQQVAIDSAT  174 (234)
Q Consensus       152 ~a~~A~~--~~~~~~---g~~i~v~~a~  174 (234)
                      +|.+|+.  ++..+.   +++|.|+||.
T Consensus       148 ~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          148 MAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9999984  555554   4999999984

>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=99.92  E-value=8e-25  Score=170.87  Aligned_cols=152  Identities=13%  Similarity=0.141  Sum_probs=103.0

Q ss_pred             ccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccch-hhhhhhhcCCCCccCC
Q 026724           10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYIS-AATRYAALGAPTLYDH   86 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   86 (234)
                      +||||||+|.+.++|++||  +++..|.|++|.|.++..+....+...... ........+.. ...++..   +..   
T Consensus        41 ~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~r~~~---~~~---  113 (205)
T 3tyt_A           41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLE-DGSCSYKDFSESRNNRFST---PEQ---  113 (205)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCT-TSCBSEEECTTCTTCSCSS---HHH---
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCccCCCcccccc-cCCccccccCCCccccccC---ccc---
Confidence            5899999999999999999  489999999999999865432111100000 00000000000 0000000   000   


Q ss_pred             CCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCce--eEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCC
Q 026724           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSH  161 (234)
Q Consensus        87 ~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v--~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~  161 (234)
                           ........++++|||+|||+++|+++|+++|++||.|  .+|+++.+.+ ++|||||+|.+.++|.+||  +++.
T Consensus       114 -----~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~  188 (205)
T 3tyt_A          114 -----AAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHY  188 (205)
T ss_dssp             -----HTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             -----ccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCC
Confidence                 0000013457899999999999999999999999999  8898885545 7799999999999999998  4777


Q ss_pred             ccCCe----EeEEEeC
Q 026724          162 EICGQ----QVAIDSA  173 (234)
Q Consensus       162 ~~~g~----~i~v~~a  173 (234)
                      .|.|+    ++.|+++
T Consensus       189 ~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          189 QMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             EECCSSSSSCEECEEE
T ss_pred             CccCCCCCcceEEEec
Confidence            88776    6777765

>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=99.92  E-value=1.7e-23  Score=171.04  Aligned_cols=75  Identities=23%  Similarity=0.336  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccC-CeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEIC-GQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~-g~~i~v~~a~  174 (234)
                      ....++|||+|||..+++++|+++|++||.|.+|.|+.+  .+|||||+|.+.++|.+|+  +++..|. |+.|+|.|++
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG--RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC--CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            446789999999999999999999999999999999854  3699999999999999998  4777888 9999999986

>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=99.91  E-value=1.3e-23  Score=166.80  Aligned_cols=150  Identities=14%  Similarity=0.267  Sum_probs=106.7

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccch-hhhhhhhcCCCCccCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYIS-AATRYAALGAPTLYDHP   87 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   87 (234)
                      +|||||+|.+.++|++||+  ++..|.|+.|.|.++.++.............   ....+.. ...+.         ..+
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~---------~~~  139 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG---LTKDYGNSPLHRF---------KKP  139 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTT---TEEECTTCSSCCC---------CST
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccc---cccccccCccccc---------CCc
Confidence            8999999999999999994  7889999999999987653221110000000   0000000 00000         000


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcC-ceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccC
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEIC  164 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~  164 (234)
                      .  .........+.++|||+|||+.+++++|+++|++|| .|..|.+++.  .++||||+|.+.++|.+|+  +++..+.
T Consensus       140 ~--~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~  215 (229)
T 2adc_A          140 G--SKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLG  215 (229)
T ss_dssp             T--SGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS--STTCEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             c--ccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC--CCcEEEEEECCHHHHHHHHHHHCCCccC
Confidence            0  000011134578999999999999999999999999 9999999743  4799999999999999998  4788999


Q ss_pred             -CeEeEEEeCCCC
Q 026724          165 -GQQVAIDSATPL  176 (234)
Q Consensus       165 -g~~i~v~~a~~~  176 (234)
                       |+.|+|.|++++
T Consensus       216 ~g~~l~v~~a~~~  228 (229)
T 2adc_A          216 ENHHLRVSFSKST  228 (229)
T ss_dssp             SSCBCEEEECSSC
T ss_pred             CCCeEEEEEecCC
Confidence             999999999874

>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=99.91  E-value=7.7e-24  Score=157.43  Aligned_cols=136  Identities=21%  Similarity=0.312  Sum_probs=108.3

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh---cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCc
Q 026724            7 SKAHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTL   83 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~---~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (234)
                      ..+.+|+++|+|.+.++|++|++   ++..|+| .|.+.++..+..........                          
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~--------------------------   61 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHH--------------------------   61 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSC--------------------------
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccc--------------------------
Confidence            45789999999999999999994   6789999 99999876532211100000                          


Q ss_pred             cCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCC
Q 026724           84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSH  161 (234)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~  161 (234)
                            ............++|||+|||+++++++|+++|++||.|.+|.|+.+  ++|||||+|.+.++|.+|+  +++.
T Consensus        62 ------~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~  133 (150)
T 2i2y_A           62 ------HHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--PPGFAFVEFEDPRDAADAVRELDGR  133 (150)
T ss_dssp             ------CCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--SCSEEEEEESSHHHHHHHHHHHSSS
T ss_pred             ------cccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--CCcEEEEEECCHHHHHHHHHHcCCC
Confidence                  00001112456789999999999999999999999999999999865  6899999999999999998  4788


Q ss_pred             ccCCeEeEEEeCCCCC
Q 026724          162 EICGQQVAIDSATPLD  177 (234)
Q Consensus       162 ~~~g~~i~v~~a~~~~  177 (234)
                      .|.|+.|+|.++.++.
T Consensus       134 ~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A          134 TLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CSSSSCCEEEECCCCC
T ss_pred             EECCeEEEEEEcCCCC
Confidence            9999999999998864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.91  E-value=1.2e-23  Score=163.27  Aligned_cols=150  Identities=14%  Similarity=0.244  Sum_probs=107.4

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccc-hhhhhhhhcCCCCccCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYI-SAATRYAALGAPTLYDHP   87 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   87 (234)
                      +|||||+|.+.++|++|+.  ++..|.|++|.|.++................   ....+. ....+.....        
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~---~~~~~~~~~~~r~~~~~--------  109 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG---LTKDYGNSPLHRFKKPG--------  109 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSSS---CEEESSCCCTTSSSSCC--------
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCcccc---ccccccCCchhhccCcc--------
Confidence            8999999999999999994  7889999999999987654221110000000   000000 0000000000        


Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcC-ceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccC
Q 026724           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEIC  164 (234)
Q Consensus        88 ~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~  164 (234)
                         .........+.++|||+|||..+++++|+++|++|| .|..|.+++.  .+|+|||+|.+.++|.+|+  +++..+.
T Consensus       110 ---~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~  184 (198)
T 1qm9_A          110 ---SKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLG  184 (198)
T ss_dssp             ---CCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST--TSSCEEEECSSHHHHHHHHHHHTSSCCS
T ss_pred             ---ccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhcCCccC
Confidence               000011134679999999999999999999999999 9999999743  4799999999999999998  4788999


Q ss_pred             -CeEeEEEeCCCC
Q 026724          165 -GQQVAIDSATPL  176 (234)
Q Consensus       165 -g~~i~v~~a~~~  176 (234)
                       |+.|+|.|++++
T Consensus       185 ~g~~l~v~~a~~~  197 (198)
T 1qm9_A          185 ENHHLRVSFSKST  197 (198)
T ss_dssp             SCCSCCEEEECCC
T ss_pred             CCCeEEEEeeccc
Confidence             999999999874

>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=99.89  E-value=1.1e-22  Score=166.33  Aligned_cols=117  Identities=17%  Similarity=0.326  Sum_probs=105.2

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      ++++|||||+|.+.++|++|+.  ++..|.|++|.|.++.                                        
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~----------------------------------------   93 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP----------------------------------------   93 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----------------------------------------
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC----------------------------------------
Confidence            6789999999999999999994  7889999999998742                                        


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcC
Q 026724           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRS  160 (234)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~  160 (234)
                                    ...+|||+|||+++++++|+++|++||.|..+.++  +.++ ++|||||+|.+.++|.+|+  +++
T Consensus        94 --------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~  159 (284)
T 3smz_A           94 --------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG  159 (284)
T ss_dssp             --------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             --------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence                          24689999999999999999999999999999888  4466 8999999999999999998  478


Q ss_pred             CccCCeEeEEEeCCCCCC
Q 026724          161 HEICGQQVAIDSATPLDD  178 (234)
Q Consensus       161 ~~~~g~~i~v~~a~~~~~  178 (234)
                      ..+.|+.|.|.++.++..
T Consensus       160 ~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          160 KPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             CEETTEECEEEECCGGGC
T ss_pred             CEeCCcEEEEEECCCCCC
Confidence            899999999999987654

>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=99.89  E-value=8.1e-23  Score=167.73  Aligned_cols=121  Identities=17%  Similarity=0.295  Sum_probs=102.3

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGA   80 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (234)
                      ++|+.+  ++|||||+|.+.++|++||+ ++..|.|++|.|.++.                                   
T Consensus        74 ~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~-----------------------------------  116 (292)
T 2ghp_A           74 ADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLT-----------------------------------  116 (292)
T ss_dssp             EECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEECC-----------------------------------
T ss_pred             EECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEECC-----------------------------------
Confidence            345543  68999999999999999994 6789999999998652                                   


Q ss_pred             CCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcC-ceeEEEeec-CCC-CcceEEEEEcChHHHHHHH
Q 026724           81 PTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPK-RTG-HRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~-~~~-~~g~afV~f~~~~~a~~A~  157 (234)
                                          .++|||+|||+.+++++|+++|++|| .|..|.++. ..+ ++|||||+|.+.++|.+|+
T Consensus       117 --------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~  176 (292)
T 2ghp_A          117 --------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV  176 (292)
T ss_dssp             --------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHH
T ss_pred             --------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHH
Confidence                                46899999999999999999999999 999999983 335 8999999999999999998


Q ss_pred             --hcCCccCCeEeEEEeCCCCCCC
Q 026724          158 --RRSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       158 --~~~~~~~g~~i~v~~a~~~~~~  179 (234)
                        +++..|.|+.|.|.++.++...
T Consensus       177 ~~l~g~~~~g~~l~v~~a~~~~~~  200 (292)
T 2ghp_A          177 EKLNGLKIEGYTLVTKVSNPLEKS  200 (292)
T ss_dssp             HHHTTCEETTEECEEEECCCC---
T ss_pred             HHhCCCEeCCcEEEEEECCCCccc
Confidence              4788999999999999877644

>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=99.89  E-value=9.5e-23  Score=164.92  Aligned_cols=118  Identities=28%  Similarity=0.381  Sum_probs=103.0

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCccC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (234)
                      .++||||||+|.+.++|++|+.  ++..|.|+.|.|.++.+                                       
T Consensus        55 ~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~---------------------------------------   95 (261)
T 3sde_A           55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH---------------------------------------   95 (261)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC---------------------------------------
T ss_pred             eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc---------------------------------------
Confidence            4679999999999999999994  78899999999998752                                       


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHhc---C
Q 026724           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSRR---S  160 (234)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~~---~  160 (234)
                                     ..+|||+|||+.+|+++|+++|++||.|..|.|+ ..++ ++|||||+|.+.++|.+|+..   +
T Consensus        96 ---------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~  160 (261)
T 3sde_A           96 ---------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDG  160 (261)
T ss_dssp             ---------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHS
T ss_pred             ---------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCC
Confidence                           4589999999999999999999999999999988 5566 899999999999999999843   3


Q ss_pred             CccC---CeEeEEEeCCCCCCC
Q 026724          161 HEIC---GQQVAIDSATPLDDA  179 (234)
Q Consensus       161 ~~~~---g~~i~v~~a~~~~~~  179 (234)
                      ..+.   +++|.|.++.+....
T Consensus       161 ~~~~~~~~r~i~v~~~~~~~~~  182 (261)
T 3sde_A          161 AFLLTTTPRPVIVEPMEQFDDE  182 (261)
T ss_dssp             CEESSSSCCBCEEEECCCEESS
T ss_pred             eEEecCCCceEEEeeccccCcc
Confidence            3333   999999999876543

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.86  E-value=2.3e-21  Score=133.84  Aligned_cols=78  Identities=27%  Similarity=0.469  Sum_probs=71.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|+|++
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999998  4567 8999999999999999998  478899999999999


Q ss_pred             CCC
Q 026724          173 ATP  175 (234)
Q Consensus       173 a~~  175 (234)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            986

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.86  E-value=4e-21  Score=143.65  Aligned_cols=83  Identities=20%  Similarity=0.318  Sum_probs=74.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++||.  +++.|.|+.|+|++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999998  4456 89999999999999999984  78899999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +.+.....
T Consensus       116 a~~~~~~~  123 (156)
T 1h2v_Z          116 DAGFKEGR  123 (156)
T ss_dssp             ESCCCTTC
T ss_pred             CCCCCCcC
Confidence            99866543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.1e-20  Score=129.06  Aligned_cols=84  Identities=35%  Similarity=0.679  Sum_probs=76.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||. +++.|.|+.|+|.++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            5578999999999999999999999999999999998  3466 89999999999999999994 788999999999999


Q ss_pred             CCCCCCCC
Q 026724          174 TPLDDAGP  181 (234)
Q Consensus       174 ~~~~~~~~  181 (234)
                      .++.....
T Consensus        87 ~~~~~~~~   94 (99)
T 2dgs_A           87 EPRDSKSS   94 (99)
T ss_dssp             CCCCCCCC
T ss_pred             CCCcccCC
Confidence            98876554

>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=3.2e-20  Score=129.02  Aligned_cols=83  Identities=33%  Similarity=0.502  Sum_probs=76.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||.+++.|+|+.|.|.++.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~   91 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPN   91 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecC
Confidence            5567899999999999999999999999999999998  3456 899999999999999999998889999999999999


Q ss_pred             CCCCCC
Q 026724          175 PLDDAG  180 (234)
Q Consensus       175 ~~~~~~  180 (234)
                      ++....
T Consensus        92 ~~~~~~   97 (103)
T 2cqg_A           92 SKQSQD   97 (103)
T ss_dssp             TTCCCC
T ss_pred             CCCcCC
Confidence            887654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=3.7e-20  Score=128.73  Aligned_cols=85  Identities=27%  Similarity=0.421  Sum_probs=75.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEE
Q 026724           97 SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAID  171 (234)
Q Consensus        97 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~  171 (234)
                      .....++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++||.  +++.|+|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            35678999999999999999999999999999999998  4456 89999999999999999984  7889999999999


Q ss_pred             eCCCCCCCCC
Q 026724          172 SATPLDDAGP  181 (234)
Q Consensus       172 ~a~~~~~~~~  181 (234)
                      ++++......
T Consensus        89 ~a~~~~~~~~   98 (103)
T 2dnm_A           89 VARYGRRDLS   98 (103)
T ss_dssp             ECSSCCSCCC
T ss_pred             ECCcCCCCCC
Confidence            9998765543

>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=99.84  E-value=6e-20  Score=126.68  Aligned_cols=84  Identities=25%  Similarity=0.375  Sum_probs=75.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++|+  ++++.|.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999998  3366 8999999999999999998  467799999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++.....
T Consensus        85 a~~~~~~~~   93 (99)
T 1whw_A           85 STIKKEASQ   93 (99)
T ss_dssp             CCCCSTTCC
T ss_pred             cCCCccccc
Confidence            998876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=8.3e-21  Score=129.05  Aligned_cols=79  Identities=32%  Similarity=0.485  Sum_probs=70.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcC-ceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhc---CCccCCeEeEEEeC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRR---SHEICGQQVAIDSA  173 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~---~~~~~g~~i~v~~a  173 (234)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|+  +.++ ++|||||+|.+.++|++||..   ...+.|++|+|++|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999998  4567 999999999999999999853   34799999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .|+...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.83  E-value=1.9e-20  Score=132.86  Aligned_cols=81  Identities=23%  Similarity=0.364  Sum_probs=72.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      ...+|||+|||+++|+++|+++|++||.|.+|+|+.+.+ ++|||||+|.+.++|++||  ++++.|+|+.|.|.++.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            356899999999999999999999999999999995556 8999999999999999998  4788999999999999887


Q ss_pred             CCCC
Q 026724          177 DDAG  180 (234)
Q Consensus       177 ~~~~  180 (234)
                      ..+.
T Consensus        84 ~~~~   87 (115)
T 4f25_A           84 KERE   87 (115)
T ss_dssp             CC--
T ss_pred             cccc
Confidence            6544

>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=99.83  E-value=9.8e-21  Score=163.16  Aligned_cols=82  Identities=28%  Similarity=0.464  Sum_probs=73.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      .+.++|||+|||+.+|+++|+++|++||.|+.|.|+  +.++ ++|||||+|.+.++|.+||  +++..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456899999999999999999999999999999998  4467 8999999999999999998  4788999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++....
T Consensus       180 ~~~~~~~  186 (437)
T 3pgw_S          180 RGRTVKG  186 (437)
T ss_pred             CCCCCCC
Confidence            9876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=7.1e-20  Score=125.32  Aligned_cols=82  Identities=29%  Similarity=0.537  Sum_probs=74.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++|+.  +++.|.|+.|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            357899999999999999999999999999999998  3456 89999999999999999984  788999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++....
T Consensus        83 ~~~~~~~   89 (95)
T 2dnz_A           83 TERLDGG   89 (95)
T ss_dssp             SCCCCCC
T ss_pred             ccccCCC
Confidence            9877654

>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=99.83  E-value=1.3e-19  Score=125.85  Aligned_cols=84  Identities=20%  Similarity=0.289  Sum_probs=75.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+.. +++||||+|.+.++|++|+  +++..|.|+.|+|.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            55679999999999999999999999999999999996555 8999999999999999998  47789999999999999


Q ss_pred             CCCCCCC
Q 026724          175 PLDDAGP  181 (234)
Q Consensus       175 ~~~~~~~  181 (234)
                      ++.....
T Consensus        92 ~~~~~~~   98 (103)
T 2cqi_A           92 TPSSQKS   98 (103)
T ss_dssp             CTTCCCC
T ss_pred             CCccccc
Confidence            8765543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=6.6e-20  Score=127.42  Aligned_cols=84  Identities=24%  Similarity=0.375  Sum_probs=76.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+++ +++||||+|.+.++|++||.  ++..|.|+.|.|.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            55788999999999999999999999999999999995577 89999999999999999984  7889999999999999


Q ss_pred             CCCCCCC
Q 026724          175 PLDDAGP  181 (234)
Q Consensus       175 ~~~~~~~  181 (234)
                      ++..+..
T Consensus        92 ~~~~~~~   98 (103)
T 2d9p_A           92 RKEERQS   98 (103)
T ss_dssp             SCCCCCC
T ss_pred             ccccCCC
Confidence            8876654

>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=99.83  E-value=1.9e-19  Score=125.09  Aligned_cols=84  Identities=31%  Similarity=0.539  Sum_probs=75.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+.. +++||||+|.+.++|++|+.  +++.|+|+.|+|.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   91 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            56689999999999999999999999999999999995555 89999999999999999984  7889999999999999


Q ss_pred             CCCCCCC
Q 026724          175 PLDDAGP  181 (234)
Q Consensus       175 ~~~~~~~  181 (234)
                      ++.....
T Consensus        92 ~~~~~~~   98 (103)
T 2cq3_A           92 ARVMTNS   98 (103)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            8876543

>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=99.83  E-value=1.1e-19  Score=126.76  Aligned_cols=84  Identities=24%  Similarity=0.477  Sum_probs=75.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+.  +++.|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            5567899999999999999999999999999999998  3466 89999999999999999984  77899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++.....
T Consensus        92 a~~~~~~~~  100 (105)
T 1x5u_A           92 ASAHNKNLS  100 (105)
T ss_dssp             TTTTSCCCC
T ss_pred             CCCCCcCCC
Confidence            998776543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=1.4e-19  Score=126.53  Aligned_cols=84  Identities=32%  Similarity=0.582  Sum_probs=75.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecC---CC-CcceEEEEEcChHHHHHHH--h-cCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---TG-HRGFGFVTFAEEVVADRVS--R-RSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~---~~-~~g~afV~f~~~~~a~~A~--~-~~~~~~g~~i~v  170 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+   ++ +++||||+|.+.++|++||  + +++.|.|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            557899999999999999999999999999999999854   66 8999999999999999998  4 678999999999


Q ss_pred             EeCCCCCCCCC
Q 026724          171 DSATPLDDAGP  181 (234)
Q Consensus       171 ~~a~~~~~~~~  181 (234)
                      .++.++.....
T Consensus        92 ~~a~~~~~~~~  102 (107)
T 2cph_A           92 EWADSEVTVQS  102 (107)
T ss_dssp             EECCCCCCCCC
T ss_pred             EeCCCCCCCCC
Confidence            99998876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=6.6e-20  Score=127.41  Aligned_cols=84  Identities=27%  Similarity=0.476  Sum_probs=75.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||.  +++.|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            5567899999999999999999999999999999998  3466 89999999999999999984  77899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++....+
T Consensus        92 a~~~~~~~~  100 (103)
T 2cq0_A           92 AKPSTNSGP  100 (103)
T ss_dssp             SSCCCCSCC
T ss_pred             CCCCCCCCC
Confidence            998876554

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

Probab=99.83  E-value=4.3e-20  Score=127.79  Aligned_cols=80  Identities=16%  Similarity=0.260  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--c--CCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--R--SHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~--~~~~~g~~i~v~~a  173 (234)
                      ..+.++|||+|||+++|+++|+++|++||.|++|.|+++   ||||||+|++.++|++|+.  +  +..|.|++|.|.++
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A   89 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS   89 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            456899999999999999999999999999999999864   8999999999999999985  3  36899999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      +++....
T Consensus        90 ~~~~~~~   96 (105)
T 1sjq_A           90 NHKELKT   96 (105)
T ss_dssp             SSSSCCC
T ss_pred             CCCCCCc
Confidence            8876554

>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=99.83  E-value=2e-19  Score=126.33  Aligned_cols=83  Identities=24%  Similarity=0.456  Sum_probs=73.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|..+..+++||||+|.+.++|++||  +++..|+|+.|+|+++++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            556789999999999999999999999999999999744337999999999999999998  477899999999999988


Q ss_pred             CCCCC
Q 026724          176 LDDAG  180 (234)
Q Consensus       176 ~~~~~  180 (234)
                      +....
T Consensus        99 ~~~~~  103 (109)
T 1x4a_A           99 GRGTG  103 (109)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.8e-19  Score=126.23  Aligned_cols=82  Identities=37%  Similarity=0.601  Sum_probs=72.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhc-CCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRR-SHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++||.. ...|.|+.|+|+++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a   93 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLA   93 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEc
Confidence            5678999999999999999999999999999999998  4466 999999999999999999953 23899999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++...
T Consensus        94 ~~~~~~   99 (116)
T 2cqd_A           94 YLGAKP   99 (116)
T ss_dssp             TTTCCC
T ss_pred             ccCCCc
Confidence            876543

>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=99.83  E-value=1.4e-19  Score=126.01  Aligned_cols=82  Identities=21%  Similarity=0.409  Sum_probs=73.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC-C-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT-G-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~-~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++|| |..|.|+  +.+ + ++|||||+|.+.++|++|| ++++.|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEE
Confidence            45678999999999999999999999999 9999998  334 6 8999999999999999999 467799999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +.++....
T Consensus        91 a~~~~~~~   98 (104)
T 1wi8_A           91 ADQAQDKD   98 (104)
T ss_dssp             CCCCCCCC
T ss_pred             ccCCCCCC
Confidence            99887654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=8.2e-20  Score=126.70  Aligned_cols=84  Identities=32%  Similarity=0.512  Sum_probs=75.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++|+  +++..|.|+.|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            5568899999999999999999999999999999998  3466 8999999999999999998  478899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++.....
T Consensus        89 a~~~~~~~~   97 (102)
T 1x5s_A           89 AGKSSDNRS   97 (102)
T ss_dssp             EECCCCCCC
T ss_pred             CCCCCCCCC
Confidence            998776543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=7.5e-20  Score=125.44  Aligned_cols=83  Identities=28%  Similarity=0.470  Sum_probs=74.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEE-Eee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~-~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      .+.++|||+|||+++++++|+++|++||.|..| .|+  +.++ +++||||+|.+.++|++|+.  +++.|.|+.|+|++
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            357899999999999999999999999999999 888  3566 89999999999999999984  77799999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++.....
T Consensus        83 a~~~~~~~~   91 (96)
T 1x5t_A           83 AFKKDSKGS   91 (96)
T ss_dssp             SCCCCCCCC
T ss_pred             ecccCCCCC
Confidence            998776543

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

Probab=99.82  E-value=7.1e-20  Score=128.73  Aligned_cols=80  Identities=18%  Similarity=0.202  Sum_probs=72.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++||  +++..|+|+.|+|.++
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            457899999999999999999999999999999998  4567 9999999999999999998  4788999999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      .....
T Consensus        84 ~~~~~   88 (110)
T 3s8s_A           84 IKGQQ   88 (110)
T ss_dssp             STTHH
T ss_pred             CCCcH
Confidence            76543

>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=2.8e-20  Score=135.68  Aligned_cols=83  Identities=27%  Similarity=0.444  Sum_probs=74.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||.  ++..|.|+.|+|++
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999998  3466 99999999999999999994  77899999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      ++++....
T Consensus       124 a~~~~~~~  131 (135)
T 2lea_A          124 ARYGRPPD  131 (135)
T ss_dssp             CCCCCCCT
T ss_pred             CCCCCCCc
Confidence            99876544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.82  E-value=3.1e-19  Score=130.75  Aligned_cols=83  Identities=23%  Similarity=0.430  Sum_probs=75.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+  +.++ ++|||||+|.+.++|.+||.  ++..|.|+.|+|++
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            5567899999999999999999999999999999998  4567 89999999999999999984  67799999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +.++..+.
T Consensus       119 a~~~~~~~  126 (139)
T 1u6f_A          119 AASGHQRP  126 (139)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            99876553

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=8.6e-20  Score=126.59  Aligned_cols=84  Identities=29%  Similarity=0.488  Sum_probs=75.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++|+  ++++.|.|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            4567899999999999999999999999999999998  3556 8999999999999999998  478899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++.....
T Consensus        89 a~~~~~~~~   97 (102)
T 2cqb_A           89 AKPMRIKES   97 (102)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCCCCCCC
Confidence            998876554

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.82  E-value=4.1e-19  Score=125.86  Aligned_cols=84  Identities=35%  Similarity=0.501  Sum_probs=75.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec--CCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.  .++ ++|||||+|.+.++|++||.  +++.|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            55688999999999999999999999999999999983  466 89999999999999999984  77899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      +.++.....
T Consensus        92 a~~~~~~~~  100 (115)
T 2dgo_A           92 ATRKPPAPK  100 (115)
T ss_dssp             SSCCCCCSC
T ss_pred             ccCCCCCCc
Confidence            998876543

>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=99.82  E-value=1.5e-19  Score=128.20  Aligned_cols=84  Identities=26%  Similarity=0.449  Sum_probs=75.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++||.  ++..|.|+.|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4467899999999999999999999999999999998  3456 89999999999999999983  78899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      ++++....+
T Consensus       102 a~~~~~~~~  110 (115)
T 2cpz_A          102 KRSKNDSKS  110 (115)
T ss_dssp             CCCSCCCCC
T ss_pred             cCCCCcCCC
Confidence            998876554

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

Probab=99.82  E-value=2e-19  Score=124.96  Aligned_cols=82  Identities=21%  Similarity=0.289  Sum_probs=73.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      ..+.++|||+|||+++++++|+++|++|| |..|.|+  +.++ ++|||||+|.+.++|++|| +++..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEe
Confidence            55678999999999999999999999997 9999998  4456 8999999999999999999 4677999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2dng_A           91 EGRKQDK   97 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCCCC
Confidence            9876554

>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=99.82  E-value=2.8e-19  Score=125.90  Aligned_cols=84  Identities=25%  Similarity=0.403  Sum_probs=75.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--c------CCccCCe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--R------SHEICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~------~~~~~g~  166 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||.  +      ++.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            5567899999999999999999999999999999998  4456 89999999999999999984  5      7899999


Q ss_pred             EeEEEeCCCCCCCCC
Q 026724          167 QVAIDSATPLDDAGP  181 (234)
Q Consensus       167 ~i~v~~a~~~~~~~~  181 (234)
                      .|+|.++.++.....
T Consensus        92 ~l~v~~a~~~~~~~~  106 (111)
T 1x4h_A           92 QLKVDLAVTRDEAAS  106 (111)
T ss_dssp             EEEEECCCCCCCCCC
T ss_pred             EEEEEECCCCccCCC
Confidence            999999998876543

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.82  E-value=2.2e-19  Score=125.16  Aligned_cols=84  Identities=26%  Similarity=0.443  Sum_probs=75.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCC---eEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICG---QQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g---~~i~v  170 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ +++||||+|.+.++|++||.  ++..+.+   +.|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            4568999999999999999999999999999999998 3356 89999999999999999984  7778888   99999


Q ss_pred             EeCCCCCCCCC
Q 026724          171 DSATPLDDAGP  181 (234)
Q Consensus       171 ~~a~~~~~~~~  181 (234)
                      .++.++.++.+
T Consensus        92 ~~a~~~~~~~~  102 (105)
T 2dnh_A           92 KFADTDKESGP  102 (105)
T ss_dssp             EESCSSCCCSC
T ss_pred             EECccCcccCC
Confidence            99998877654

>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=99.82  E-value=2.4e-19  Score=127.26  Aligned_cols=82  Identities=26%  Similarity=0.479  Sum_probs=73.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ ++|||||+|.+.++|++|+.  ++..|.|+.|+|+++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            3457899999999999999999999999999999998 3366 99999999999999999984  778999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      +++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

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

Probab=99.82  E-value=9.8e-20  Score=123.86  Aligned_cols=82  Identities=24%  Similarity=0.411  Sum_probs=75.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+++ +++||||+|.+.++|++|+.  ++..|.|+.|+|++++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45678999999999999999999999999999999997677 89999999999999999984  7889999999999999


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      +....
T Consensus        85 ~~~~~   89 (92)
T 2dgv_A           85 NASGP   89 (92)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87654

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

Probab=99.82  E-value=2.3e-19  Score=124.02  Aligned_cols=82  Identities=20%  Similarity=0.343  Sum_probs=74.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ +++||||+|.+.++|++|+.  ++..|.|+.|+|.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            4567899999999999999999999999999999998 3356 89999999999999999983  778999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++..+
T Consensus        94 ~~~~~~   99 (100)
T 2do4_A           94 NSGPSS   99 (100)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            987653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=6.7e-20  Score=127.83  Aligned_cols=84  Identities=35%  Similarity=0.563  Sum_probs=75.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||. +++.|+|+.|+|.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEc
Confidence            5668999999999999999999999999999999998  3566 89999999999999999985 777999999999999


Q ss_pred             CCCCCCCC
Q 026724          174 TPLDDAGP  181 (234)
Q Consensus       174 ~~~~~~~~  181 (234)
                      .++.....
T Consensus        93 ~~~~~~~~  100 (105)
T 2dh8_A           93 TPRGMQPS  100 (105)
T ss_dssp             CCSSCCTT
T ss_pred             cCCCCCCC
Confidence            98876543

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.82  E-value=9.8e-21  Score=150.02  Aligned_cols=77  Identities=22%  Similarity=0.398  Sum_probs=69.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcC--ceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..++|||+||++++|+++|+++|++||  .|++|.|+  +.++ ++|||||+|.+.++|++||.  +++.|.|+.|+|++
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            567999999999999999999999999  99999998  4577 99999999999999999994  67899999999999


Q ss_pred             CCCC
Q 026724          173 ATPL  176 (234)
Q Consensus       173 a~~~  176 (234)
                      +.++
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8754

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

Probab=99.82  E-value=6.6e-20  Score=125.33  Aligned_cols=78  Identities=19%  Similarity=0.376  Sum_probs=68.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCc--eeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCC----ccCCe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSH----EICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~--v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~----~~~g~  166 (234)
                      .....+|||+|||+++|+++|+++|++||.  |.+|+|+  +.++ ++|||||+|.+.++|++||.  ++.    .|+|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            456789999999999999999999999995  5688888  4567 99999999999999999984  443    59999


Q ss_pred             EeEEEeCCC
Q 026724          167 QVAIDSATP  175 (234)
Q Consensus       167 ~i~v~~a~~  175 (234)
                      +|.|+||++
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999975

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=1.5e-19  Score=124.43  Aligned_cols=83  Identities=22%  Similarity=0.393  Sum_probs=73.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cC---CC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEE
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KR---TG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAI  170 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~---~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v  170 (234)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+  +.   ++ +++||||+|.+.++|++|+.  +++.|.|+.|.|
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            357899999999999999999999999999999988  33   55 88999999999999999984  778999999999


Q ss_pred             EeCCCCCCCCC
Q 026724          171 DSATPLDDAGP  181 (234)
Q Consensus       171 ~~a~~~~~~~~  181 (234)
                      +++.++.....
T Consensus        83 ~~a~~~~~~~~   93 (98)
T 2cpf_A           83 RISERATKPAS   93 (98)
T ss_dssp             ECSSCSSCCCC
T ss_pred             EEccCCCCCCC
Confidence            99998765543

>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=99.81  E-value=2.2e-19  Score=125.36  Aligned_cols=83  Identities=25%  Similarity=0.537  Sum_probs=73.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCcc---CCeEeE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEI---CGQQVA  169 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~---~g~~i~  169 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+  +++..+   .++.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            5567899999999999999999999999999999998  4456 8999999999999999998  466666   889999


Q ss_pred             EEeCCCCCCCC
Q 026724          170 IDSATPLDDAG  180 (234)
Q Consensus       170 v~~a~~~~~~~  180 (234)
                      |.++.++....
T Consensus        90 v~~a~~~~~~~  100 (106)
T 2dgp_A           90 VKPADSESRGG  100 (106)
T ss_dssp             EEECCCCSCCC
T ss_pred             EEECCcccccC
Confidence            99999877654

>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=99.81  E-value=6.3e-19  Score=122.46  Aligned_cols=79  Identities=27%  Similarity=0.393  Sum_probs=71.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+     ++||||+|.+.++|++||.  +++.|.|+.|.|.++.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   82 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP   82 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCC
Confidence            4567899999999999999999999999999999985     5799999999999999984  78899999999999998


Q ss_pred             CCCCCC
Q 026724          176 LDDAGP  181 (234)
Q Consensus       176 ~~~~~~  181 (234)
                      +.....
T Consensus        83 ~~~~~~   88 (103)
T 2dgu_A           83 PDQKRK   88 (103)
T ss_dssp             CCCCCC
T ss_pred             Ccccch
Confidence            776543

>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=99.81  E-value=5.1e-19  Score=122.25  Aligned_cols=80  Identities=16%  Similarity=0.237  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh----cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR----RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~----~~~~~~g~~i~v~~a  173 (234)
                      ..++++|||+|||+++++++|+++|++||.|.+|.|+++   +|||||+|++.++|.+|+.    +...|.|++|.|.++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            456789999999999999999999999999999988864   8999999999999999985    345799999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      +++....
T Consensus        89 ~~~~~~~   95 (101)
T 2cq1_A           89 NHKELKT   95 (101)
T ss_dssp             SCSSCCC
T ss_pred             CcccCcC
Confidence            9876544

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

Probab=99.81  E-value=2.7e-19  Score=122.59  Aligned_cols=77  Identities=18%  Similarity=0.216  Sum_probs=69.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCC--ccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSH--EICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~--~~~g~~i~v~~a  173 (234)
                      ..++++|||+|||+++|+++|+++|++||.|.+|.+++   .||||||+|++.++|.+|+.  ++.  .|.|++|.|.++
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~---~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S   94 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS   94 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEec
Confidence            45788999999999999999999999999999999986   37999999999999999985  444  488999999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      ++++
T Consensus        95 ~~k~   98 (100)
T 3r27_A           95 TSQK   98 (100)
T ss_dssp             SCSC
T ss_pred             cccc
Confidence            8764

>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=2e-19  Score=124.31  Aligned_cols=80  Identities=11%  Similarity=0.159  Sum_probs=70.2

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cC--CccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RS--HEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~--~~~~g~~i~v~~  172 (234)
                      ..++++|||+|||+ ++|+++|+++|++||.|.+|.|+++   ++||||+|++.++|.+|+.  ++  ..|.|++|.|.+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   88 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            34678999999999 9999999999999999999999864   6899999999999999985  43  369999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +++...-.
T Consensus        89 a~~~~~~~   96 (102)
T 1x4d_A           89 SQKYKRIK   96 (102)
T ss_dssp             ECCCTTSS
T ss_pred             CCCCCCCC
Confidence            98765443

>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=99.81  E-value=9.5e-19  Score=122.63  Aligned_cols=78  Identities=18%  Similarity=0.287  Sum_probs=70.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCC-----eEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICG-----QQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g-----~~i~v  170 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+    +||||+|.+.++|++||.  ++..|.|     +.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            456889999999999999999999999999999999854    899999999999999984  6778999     99999


Q ss_pred             EeCCCCCCC
Q 026724          171 DSATPLDDA  179 (234)
Q Consensus       171 ~~a~~~~~~  179 (234)
                      +++.++...
T Consensus        88 ~~a~~~~~~   96 (108)
T 1x4c_A           88 KVDGPRSPS   96 (108)
T ss_dssp             EESSCCSCC
T ss_pred             EeCCCCCCC
Confidence            999986654

>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=99.81  E-value=2.3e-19  Score=119.64  Aligned_cols=76  Identities=32%  Similarity=0.520  Sum_probs=70.3

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~  176 (234)
                      .+|||+|||+++++++|+++|++||.|.+|.++  +.++ ++|||||+|.+.++|++|+.  ++..+.|+.|+|+++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            589999999999999999999999999999998  3466 89999999999999999984  788999999999999987


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.81  E-value=1.7e-19  Score=121.37  Aligned_cols=78  Identities=32%  Similarity=0.475  Sum_probs=69.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      .+.++|||+|||+++++++|+++|++||.|.+|.++  +.++ ++|||||+|.+.++|++|+.  ++..+.|+.|+|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            357899999999999999999999999999999998  3466 89999999999999999984  788999999999999


Q ss_pred             CCC
Q 026724          174 TPL  176 (234)
Q Consensus       174 ~~~  176 (234)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            876

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.8e-19  Score=125.09  Aligned_cols=83  Identities=19%  Similarity=0.314  Sum_probs=74.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCcee--------EEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL--------DVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--------~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~  164 (234)
                      ....++|||+|||+++++++|+++|++||.|.        .|.|+  +.++ ++|||||+|.+.++|++||.  +++.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            55689999999999999999999999999998        58888  3567 89999999999999999984  788999


Q ss_pred             CeEeEEEeCCCCCCCC
Q 026724          165 GQQVAIDSATPLDDAG  180 (234)
Q Consensus       165 g~~i~v~~a~~~~~~~  180 (234)
                      |+.|+|.+++++....
T Consensus        92 g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           92 GSKLKVSLARKKPPMN  107 (113)
T ss_dssp             TEECEEECSSCCCCST
T ss_pred             CCEEEEEECCCCCCCC
Confidence            9999999999877654

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

Probab=99.80  E-value=2.9e-19  Score=126.82  Aligned_cols=83  Identities=35%  Similarity=0.604  Sum_probs=74.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSAT  174 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~  174 (234)
                      ...++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||. +++.|+|+.|+|.++.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECC
Confidence            345899999999999999999999999999999998  4556 89999999999999999995 6679999999999999


Q ss_pred             CCCCCCC
Q 026724          175 PLDDAGP  181 (234)
Q Consensus       175 ~~~~~~~  181 (234)
                      ++.....
T Consensus       105 ~~~~~~~  111 (116)
T 1x4b_A          105 AREESGS  111 (116)
T ss_dssp             SCCCCCC
T ss_pred             CCccCCC
Confidence            8876543

>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=99.80  E-value=6.3e-19  Score=122.71  Aligned_cols=82  Identities=18%  Similarity=0.314  Sum_probs=72.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|.. |.|+ ..++ ++|||||+|.+.++|++||. +++.|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            456789999999999999999999999999987 7777 5466 89999999999999999995 677999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .+++-.
T Consensus        92 ~~~~~~   97 (104)
T 1wg5_A           92 SRAEVR   97 (104)
T ss_dssp             CTTTSC
T ss_pred             CHHHHH
Confidence            876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=5e-19  Score=120.80  Aligned_cols=77  Identities=26%  Similarity=0.509  Sum_probs=70.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+  +.++ +++||||+|.+.++|++|+.  ++..|.|+.|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            5567899999999999999999999999999999998  4456 89999999999999999984  77899999999999


Q ss_pred             CC
Q 026724          173 AT  174 (234)
Q Consensus       173 a~  174 (234)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

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

Probab=99.80  E-value=3.5e-19  Score=123.91  Aligned_cols=84  Identities=23%  Similarity=0.388  Sum_probs=74.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhh-cCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCc-cCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSR-FGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHE-ICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~-~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~-~~g~~i~v~  171 (234)
                      ..+.++|||+|||+++++++|+++|++ ||.|..|.|+ ..++ ++|||||+|.+.++|.+||.  ++.. |+|+.|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            456789999999999999999999999 9999999998 3366 89999999999999999985  6667 999999999


Q ss_pred             eCCCCCCCCC
Q 026724          172 SATPLDDAGP  181 (234)
Q Consensus       172 ~a~~~~~~~~  181 (234)
                      ++.++.....
T Consensus        86 ~a~~~~~~~~   95 (104)
T 2dhg_A           86 VAIPKASRVK   95 (104)
T ss_dssp             BCCCCCSCCC
T ss_pred             EccCCCcCCC
Confidence            9988766543

>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=99.80  E-value=2e-19  Score=129.53  Aligned_cols=82  Identities=24%  Similarity=0.423  Sum_probs=74.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||  +++..|.|+.|.|++
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4567899999999999999999999999999999998  3466 8999999999999999998  478899999999999


Q ss_pred             CCCCCCC
Q 026724          173 ATPLDDA  179 (234)
Q Consensus       173 a~~~~~~  179 (234)
                      +.++...
T Consensus        99 a~~~~~~  105 (126)
T 3ex7_B           99 CFVRGPP  105 (126)
T ss_dssp             SEESSSC
T ss_pred             ecCCCCC
Confidence            9877654

>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=99.80  E-value=1.8e-19  Score=135.89  Aligned_cols=83  Identities=23%  Similarity=0.406  Sum_probs=72.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|.+||  +++..|.|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999998  4567 8999999999999999998  478899999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +.++....
T Consensus       149 a~~~~~~~  156 (165)
T 1rk8_A          149 CFVKGPKR  156 (165)
T ss_dssp             SEECC---
T ss_pred             ecCCCCCC
Confidence            98876544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=2e-18  Score=122.11  Aligned_cols=83  Identities=22%  Similarity=0.370  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ +++||||+|.+.++|++||.  +++.|+|+.|+|+++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            4567899999999999999999999999999999998 3456 89999999999999999984  788999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .+.....
T Consensus        92 ~~~~~~~   98 (114)
T 2do0_A           92 ERALPKG   98 (114)
T ss_dssp             SCCCCCS
T ss_pred             ccCCCCC
Confidence            8655443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=8.1e-19  Score=119.36  Aligned_cols=79  Identities=18%  Similarity=0.358  Sum_probs=71.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.++     ++||||+|.+.++|++|+  ++++.|.|+.|+|+++.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   81 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS   81 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-----SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccC
Confidence            5567899999999999999999999999999999996     569999999999999998  478899999999999998


Q ss_pred             CCCCCC
Q 026724          176 LDDAGP  181 (234)
Q Consensus       176 ~~~~~~  181 (234)
                      +....+
T Consensus        82 ~~~~~~   87 (92)
T 2dgt_A           82 RLRTAS   87 (92)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            766543

>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=99.80  E-value=3.8e-19  Score=119.71  Aligned_cols=76  Identities=32%  Similarity=0.688  Sum_probs=69.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+. +++.|+|+.|.|++|
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4567899999999999999999999999999999998  4556 89999999999999999994 567899999999986

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

Probab=99.80  E-value=7.9e-19  Score=118.91  Aligned_cols=78  Identities=23%  Similarity=0.541  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.++     ++||||+|.+.++|++|+  +++..|+|+.|+|+++.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   79 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN   79 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCC
Confidence            4567899999999999999999999999999999996     689999999999999998  477799999999999998


Q ss_pred             CCCCC
Q 026724          176 LDDAG  180 (234)
Q Consensus       176 ~~~~~  180 (234)
                      +....
T Consensus        80 ~~~~~   84 (90)
T 2dnq_A           80 KSKAS   84 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>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=99.80  E-value=7.5e-19  Score=120.53  Aligned_cols=82  Identities=16%  Similarity=0.170  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHH----HHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~  171 (234)
                      ....++|||+|||+++++++|+    ++|++||.|.+|.|+.+...++||||+|.+.++|++|+  +++..|.|+.|+|+
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456899999999999999999    99999999999999833223899999999999999998  47789999999999


Q ss_pred             eCCCCCCC
Q 026724          172 SATPLDDA  179 (234)
Q Consensus       172 ~a~~~~~~  179 (234)
                      ++++....
T Consensus        86 ~a~~~~~~   93 (96)
T 2dgx_A           86 LATGASGP   93 (96)
T ss_dssp             ECCCSSCC
T ss_pred             EcCCCCCC
Confidence            99877654

>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=99.80  E-value=1.7e-18  Score=120.26  Aligned_cols=80  Identities=20%  Similarity=0.189  Sum_probs=70.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cC--CccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RS--HEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~--~~~~g~~i~v~~a  173 (234)
                      ..++++|||+|||+++++++|+++|++||.|.+|.|++.   |+||||+|++.++|.+|+.  ++  ..|.|++|.|.++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF---KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            456789999999999999999999999999999998864   7999999999999999985  33  4699999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      +++....
T Consensus        89 ~~~~~~~   95 (104)
T 1wex_A           89 TSKRITR   95 (104)
T ss_dssp             SSSSCCC
T ss_pred             cCccccC
Confidence            8876543

>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=99.80  E-value=5.2e-19  Score=121.31  Aligned_cols=78  Identities=15%  Similarity=0.368  Sum_probs=71.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      +++|||+|||+++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|+  +++..+.|+.|+|.++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            6799999999999999999999999999999998  3456 8999999999999999998  478899999999999998


Q ss_pred             CCC
Q 026724          176 LDD  178 (234)
Q Consensus       176 ~~~  178 (234)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            753

>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=99.80  E-value=3e-19  Score=123.86  Aligned_cols=79  Identities=20%  Similarity=0.243  Sum_probs=70.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++|+++|+++|++||.+ .|.|+ ..++ ++|||||+|.+.++|++|| ++.+.|.++.|+|.++.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            4567899999999999999999999999955 88888 4466 9999999999999999999 46779999999999988


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      +..
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            655

>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=99.80  E-value=5.9e-19  Score=118.16  Aligned_cols=77  Identities=30%  Similarity=0.508  Sum_probs=70.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++  +.++ +++||||+|.+.++|.+|+  +++..+.|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999998  4666 8999999999999999998  478899999999999


Q ss_pred             CC
Q 026724          173 AT  174 (234)
Q Consensus       173 a~  174 (234)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

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

Probab=99.80  E-value=2.9e-19  Score=124.79  Aligned_cols=81  Identities=25%  Similarity=0.427  Sum_probs=73.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+  ++++.|.|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            4557899999999999999999999999999999998  4556 8999999999999999998  478899999999999


Q ss_pred             CCCCCC
Q 026724          173 ATPLDD  178 (234)
Q Consensus       173 a~~~~~  178 (234)
                      +.++.+
T Consensus       100 a~~~~~  105 (106)
T 1p27_B          100 CFVRGP  105 (106)
T ss_dssp             SEESSC
T ss_pred             ecCCCC
Confidence            987654

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

Probab=99.80  E-value=4e-19  Score=124.77  Aligned_cols=79  Identities=33%  Similarity=0.587  Sum_probs=72.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.+.+ ++|||||+|.+.++|++|+.  ++..|+|+.|+|+++.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  105 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT  105 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            55788999999999999999999999999999999985555 89999999999999999984  7889999999999998


Q ss_pred             CC
Q 026724          175 PL  176 (234)
Q Consensus       175 ~~  176 (234)
                      ++
T Consensus       106 ~~  107 (109)
T 2err_A          106 AR  107 (109)
T ss_dssp             CS
T ss_pred             CC
Confidence            76

>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=99.80  E-value=3.8e-19  Score=125.03  Aligned_cols=82  Identities=23%  Similarity=0.415  Sum_probs=74.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999998  4566 8999999999999999998  478899999999999


Q ss_pred             CCCCCCC
Q 026724          173 ATPLDDA  179 (234)
Q Consensus       173 a~~~~~~  179 (234)
                      +.++.++
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9887643

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.79  E-value=7.4e-19  Score=123.38  Aligned_cols=82  Identities=35%  Similarity=0.585  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||. .++.|+|+.|.|.++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            4567899999999999999999999999999999998  4457 99999999999999999995 347999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++..+
T Consensus       102 ~~~~~~  107 (109)
T 2rs2_A          102 FPRRAQ  107 (109)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987654

>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=99.79  E-value=9.4e-19  Score=122.64  Aligned_cols=80  Identities=28%  Similarity=0.510  Sum_probs=73.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            5567899999999999999999999999999999998  4567 8999999999999999998  478899999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98875

>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=99.79  E-value=1.1e-18  Score=117.80  Aligned_cols=77  Identities=23%  Similarity=0.393  Sum_probs=70.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~~  176 (234)
                      .++|||+|||+++++++|+++|++||.|..|.++  +.++ ++|||||+|.+.++|++|+ ++++.+.|+.|+|.++++.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            5799999999999999999999999999999998  3466 8999999999999999998 4678999999999999875


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      .
T Consensus        86 ~   86 (89)
T 3ucg_A           86 R   86 (89)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.79  E-value=5.2e-19  Score=127.85  Aligned_cols=81  Identities=27%  Similarity=0.362  Sum_probs=73.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++||.  ++..|+|+.|.|++
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5567899999999999999999999999999999998  4556 89999999999999999984  78899999999999


Q ss_pred             CCCCCC
Q 026724          173 ATPLDD  178 (234)
Q Consensus       173 a~~~~~  178 (234)
                      +.++.+
T Consensus       123 a~~~~p  128 (129)
T 2kxn_B          123 SITKRP  128 (129)
T ss_dssp             CSSSSC
T ss_pred             ecCCCC
Confidence            998764

>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=99.79  E-value=9.3e-19  Score=123.99  Aligned_cols=80  Identities=16%  Similarity=0.260  Sum_probs=71.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--c--CCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--R--SHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~--~~~~~g~~i~v~~a  173 (234)
                      ..++++|||+|||+++++++|+++|++||.|++|.|+++   +|||||+|++.++|.+|+.  +  +..|.|++|.|.++
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~---kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a  104 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS  104 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG---GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEc
Confidence            456789999999999999999999999999999999864   7999999999999999985  3  35899999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      +++....
T Consensus       105 ~~k~~~~  111 (119)
T 2ad9_A          105 NHKELKT  111 (119)
T ss_dssp             SSSSCCC
T ss_pred             cCCCCCc
Confidence            9877554

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=9.8e-19  Score=118.67  Aligned_cols=80  Identities=11%  Similarity=0.249  Sum_probs=72.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++| .|..|.|+ ..++ ++|||||+|.+.++|++||. ++..|.|+.|.|.++.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            4567899999999999999999999999 99999998 4456 89999999999999999995 6679999999999998


Q ss_pred             CCCC
Q 026724          175 PLDD  178 (234)
Q Consensus       175 ~~~~  178 (234)
                      ++..
T Consensus        86 ~~~~   89 (91)
T 2dgw_A           86 SGPS   89 (91)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            8754

>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=99.79  E-value=9.8e-20  Score=123.46  Aligned_cols=79  Identities=23%  Similarity=0.424  Sum_probs=65.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcC--ceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      .+|||+|||+++++++|+++|++||  .|.+|.|+  +.++ ++|||||+|.+.++|++|+  +++..|+|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999988  4577 9999999999999999998  57889999999999999


Q ss_pred             CCCCCC
Q 026724          175 PLDDAG  180 (234)
Q Consensus       175 ~~~~~~  180 (234)
                      +.....
T Consensus        82 ~~~~~~   87 (90)
T 3p5t_L           82 KLEHHH   87 (90)
T ss_dssp             ------
T ss_pred             CCcccc
Confidence            876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=8.1e-19  Score=119.97  Aligned_cols=78  Identities=27%  Similarity=0.392  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++  +.++ +++||||+|.+.++|++|+.  ++..|.|+.|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999998  4456 89999999999999999984  77899999999999


Q ss_pred             CCC
Q 026724          173 ATP  175 (234)
Q Consensus       173 a~~  175 (234)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            874

>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=99.79  E-value=4.1e-19  Score=119.82  Aligned_cols=80  Identities=35%  Similarity=0.682  Sum_probs=71.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCCCCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDD  178 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~~~~~  178 (234)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+  ++|||||+|.+.++|++|+.....+.++.|.|.++.++..
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--CCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC--CCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCCCCC
Confidence            35789999999999999999999999999999999854  6899999999999999876666678999999999998876


Q ss_pred             CC
Q 026724          179 AG  180 (234)
Q Consensus       179 ~~  180 (234)
                      ..
T Consensus        81 ~~   82 (88)
T 1wf0_A           81 SN   82 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.79  E-value=3.6e-19  Score=123.59  Aligned_cols=78  Identities=15%  Similarity=0.316  Sum_probs=69.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec-CCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~-~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+. ..+ ++|||||+|.+.++|.+||. +++.|+|+.|.|.++.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            44568999999999999999999999999999999992 236 99999999999999999994 6789999999999875


Q ss_pred             C
Q 026724          175 P  175 (234)
Q Consensus       175 ~  175 (234)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.79  E-value=6.3e-19  Score=119.19  Aligned_cols=79  Identities=39%  Similarity=0.753  Sum_probs=65.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCCCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..+..+|||+|||+++|+++|+++|++||.|.+|.|+.+  ++|||||+|.+.++|+++....+.+.|+.|.|.++.++.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~--srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP--FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS--CCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEECC---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC--CCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEEcCCCC
Confidence            556889999999999999999999999999999999864  799999999999999965444556789999999999876


Q ss_pred             C
Q 026724          178 D  178 (234)
Q Consensus       178 ~  178 (234)
                      .
T Consensus        86 ~   86 (89)
T 3d2w_A           86 N   86 (89)
T ss_dssp             -
T ss_pred             c
Confidence            4

>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=99.79  E-value=2.1e-18  Score=118.51  Aligned_cols=78  Identities=21%  Similarity=0.345  Sum_probs=70.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccC--CeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEIC--GQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~--g~~i~v~~a  173 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++..   ++||||+|.+.++|++|+.  ++..|.  |+.|+|+++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a   90 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEEC
Confidence            456789999999999999999999999999999998754   7899999999999999984  778999  999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      +++..
T Consensus        91 ~~~~~   95 (97)
T 1why_A           91 KSGPS   95 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98764

>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=99.79  E-value=8.3e-19  Score=118.16  Aligned_cols=79  Identities=22%  Similarity=0.431  Sum_probs=70.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC-C-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT-G-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~-~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ..++|||+|||+++++++|+++|++||.|..|.|+  +.+ + ++|||||+|.+.++|++|+.  ++..++|+.|+|+++
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            46899999999999999999999999999999998  222 3 78999999999999999984  788999999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      .+..+
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.79  E-value=1.1e-18  Score=122.35  Aligned_cols=80  Identities=15%  Similarity=0.245  Sum_probs=70.9

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--c--CCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--R--SHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~--~~~~~g~~i~v~~  172 (234)
                      ..++++|||+|||++ +++++|+++|++||.|.+|.|++   ++|||||+|++.++|.+|+.  +  ...|.|++|.|.+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   98 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            446889999999998 99999999999999999999986   48999999999999999985  3  3469999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      ++++....
T Consensus        99 a~~~~~~~  106 (112)
T 1x4f_A           99 SEKYKKLV  106 (112)
T ss_dssp             ECSCSSSS
T ss_pred             Cccccccc
Confidence            98776554

>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=99.78  E-value=2.2e-18  Score=118.78  Aligned_cols=80  Identities=25%  Similarity=0.544  Sum_probs=72.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++++   ++||||+|.+.++|++|+  ++++.|.|+.|+|.++.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~---kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   88 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT---TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCC
Confidence            556789999999999999999999999999999999864   799999999999999998  478899999999999998


Q ss_pred             CCCCC
Q 026724          176 LDDAG  180 (234)
Q Consensus       176 ~~~~~  180 (234)
                      +....
T Consensus        89 ~~~~~   93 (99)
T 2cpj_A           89 SASLT   93 (99)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            76543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=7.6e-19  Score=121.10  Aligned_cols=81  Identities=21%  Similarity=0.372  Sum_probs=72.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCcee-EEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeE----
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL-DVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQ----  167 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~-~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~----  167 (234)
                      ....++|||+|||+++++++|+++|++||.|. .|.|+  +.++ ++|||||+|.+.++|++|+.  ++..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45689999999999999999999999999999 99998  4466 89999999999999999984  677999999    


Q ss_pred             eEEEeCCCCCC
Q 026724          168 VAIDSATPLDD  178 (234)
Q Consensus       168 i~v~~a~~~~~  178 (234)
                      |+|.++.+...
T Consensus        86 l~v~~a~~~~~   96 (99)
T 2div_A           86 FKLNYATYSGP   96 (99)
T ss_dssp             CCEEETTCCSS
T ss_pred             EEEeecCCCCC
Confidence            99999987643

>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=99.78  E-value=1e-19  Score=132.90  Aligned_cols=80  Identities=19%  Similarity=0.233  Sum_probs=69.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++|+++|+++|++|| |++|.|+ ..++ ++|||||+|.+.++|++|| ++.+.|.++.|+|..+.
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            34578999999999999999999999999 6689888 3336 9999999999999999999 46779999999999998


Q ss_pred             CCCC
Q 026724          175 PLDD  178 (234)
Q Consensus       175 ~~~~  178 (234)
                      ++..
T Consensus       122 ~~~~  125 (139)
T 2hgn_A          122 TTGA  125 (139)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=5e-18  Score=116.99  Aligned_cols=78  Identities=21%  Similarity=0.310  Sum_probs=70.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhc--CceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRF--GRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++|  |.|..|.++     ++||||+|.+.++|++|+  +++..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   86 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-----CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            5567899999999999999999999999  999999884     689999999999999998  4788999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      +++....
T Consensus        87 ~~~~~~~   93 (99)
T 2cpd_A           87 KPVDKDS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.78  E-value=8.6e-19  Score=119.88  Aligned_cols=78  Identities=22%  Similarity=0.425  Sum_probs=70.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ +++||||+|.+.++|++|+.  +++.|.|+.|+|+++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            4567899999999999999999999999999999998 3345 89999999999999999984  788999999999998


Q ss_pred             CC
Q 026724          174 TP  175 (234)
Q Consensus       174 ~~  175 (234)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=2.2e-18  Score=119.19  Aligned_cols=80  Identities=25%  Similarity=0.415  Sum_probs=69.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|   .++ ..++ +++||||+|.+.++|++||.  +++.|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            5568999999999999999999999999987   445 3455 89999999999999999984  677999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++....
T Consensus        89 ~~~~~~~   95 (101)
T 2fc9_A           89 GPRGSPN   95 (101)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9875543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=1.3e-18  Score=115.36  Aligned_cols=72  Identities=10%  Similarity=0.194  Sum_probs=67.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      .+..|||+||++.+||++|+++|.+||+|.++.+..   ++|||||+|.+.++|++|+  +|+..+.|++|+|++|.
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            467899999999999999999999999999999875   5899999999999999998  57889999999999984

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.78  E-value=8.4e-19  Score=127.18  Aligned_cols=82  Identities=18%  Similarity=0.289  Sum_probs=72.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE--EEee--cCCC-CcceEEEEEcChHHHHHHH--hcCC----ccCCe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSH----EICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~----~~~g~  166 (234)
                      ....++|||+|||+++|+++|+++|++||.|..  |+|+  +.++ ++|||||+|.+. +|.+|+  +++.    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            556789999999999999999999999999976  8888  4467 999999999999 999998  4777    99999


Q ss_pred             EeEEEeCCCCCCCC
Q 026724          167 QVAIDSATPLDDAG  180 (234)
Q Consensus       167 ~i~v~~a~~~~~~~  180 (234)
                      .|.|+++.++....
T Consensus        99 ~l~V~~a~~~~~~~  112 (131)
T 2m2b_A           99 TINVEFAKGSKRDM  112 (131)
T ss_dssp             CCCCEECCCSCCCC
T ss_pred             EEEEEECCCCCCCC
Confidence            99999999875543

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

Probab=99.78  E-value=3.1e-18  Score=115.94  Aligned_cols=78  Identities=26%  Similarity=0.454  Sum_probs=70.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.++     ++||||+|.+.++|++|+.  ++..|+|+.|+|.++.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   80 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK   80 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCC
Confidence            4567899999999999999999999999999999996     5699999999999999984  78899999999999998


Q ss_pred             CCCCC
Q 026724          176 LDDAG  180 (234)
Q Consensus       176 ~~~~~  180 (234)
                      +....
T Consensus        81 ~~~~~   85 (90)
T 2dnp_A           81 GQKKS   85 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            75543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.78  E-value=1.7e-18  Score=119.38  Aligned_cols=77  Identities=26%  Similarity=0.390  Sum_probs=70.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE--------EEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~  164 (234)
                      ....++|||+|||+++++++|+++|++||.|..        |.|+  +.++ ++|||||+|.+.++|++|+  +++..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            567899999999999999999999999999999        8888  4567 8999999999999999998  4788999


Q ss_pred             CeEeEEEeCC
Q 026724          165 GQQVAIDSAT  174 (234)
Q Consensus       165 g~~i~v~~a~  174 (234)
                      |+.|+|++|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999984

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.78  E-value=1.8e-18  Score=120.54  Aligned_cols=81  Identities=23%  Similarity=0.441  Sum_probs=72.8

Q ss_pred             CCCCCEEEEeCCCCCC------CHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCe-E
Q 026724           98 QRIGKKIFVGRLPQEA------TAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQ-Q  167 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~------~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~-~  167 (234)
                      ....++|||+|||+.+      ++++|+++|++||.|..|.|++.++ ++|||||+|.+.++|.+|+.  ++..|.|+ .
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            4457899999999999      7899999999999999999987777 99999999999999999984  77899998 9


Q ss_pred             eEEEeCCCCCC
Q 026724          168 VAIDSATPLDD  178 (234)
Q Consensus       168 i~v~~a~~~~~  178 (234)
                      |+|.++.....
T Consensus        92 l~V~~a~~~~k  102 (105)
T 2nlw_A           92 FRVNLFTDFDK  102 (105)
T ss_dssp             EEEECSCCCCC
T ss_pred             EEEEEcchHhh
Confidence            99999986543

>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=99.78  E-value=3.5e-18  Score=119.87  Aligned_cols=81  Identities=22%  Similarity=0.347  Sum_probs=73.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+   ++||||+|.+.++|++|+  +++..|.|+.|+|.++++
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   98 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   98 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCC
Confidence            446789999999999999999999999999999999864   799999999999999998  478899999999999998


Q ss_pred             CCCCCC
Q 026724          176 LDDAGP  181 (234)
Q Consensus       176 ~~~~~~  181 (234)
                      +.....
T Consensus        99 ~~~~~~  104 (109)
T 1x4g_A           99 SPDMTS  104 (109)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            775543

>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=99.78  E-value=4.9e-18  Score=119.09  Aligned_cols=83  Identities=27%  Similarity=0.443  Sum_probs=72.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCc-eeEEEee---cCCC-CcceEEEEEcChHHHHHHHh--c--CCccCCeEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVP---KRTG-HRGFGFVTFAEEVVADRVSR--R--SHEICGQQV  168 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~---~~~~-~~g~afV~f~~~~~a~~A~~--~--~~~~~g~~i  168 (234)
                      ....++|||+|||+++++++|+++|++||. |..|.++   +.++ ++|||||+|.+.++|++|+.  +  ...++|+.|
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            445789999999999999999999999998 9999887   3455 89999999999999999984  3  378999999


Q ss_pred             EEEeCCCCCCCC
Q 026724          169 AIDSATPLDDAG  180 (234)
Q Consensus       169 ~v~~a~~~~~~~  180 (234)
                      +|.++.++....
T Consensus        85 ~V~~a~~~~~~~   96 (109)
T 2dis_A           85 AVDWAEPEIDVD   96 (109)
T ss_dssp             EEEESCSSCSTT
T ss_pred             EEEEcCCCCCcC
Confidence            999999876543

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

Probab=99.77  E-value=6.3e-19  Score=115.24  Aligned_cols=71  Identities=45%  Similarity=0.763  Sum_probs=65.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      +|||+|||+++++++|+++|++||.|..|.++  +.++ ++|||||+|.+.++|++|+ ++++.++|+.|.|++|
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999988  3466 8999999999999999998 4778999999999886

>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=99.77  E-value=1.4e-18  Score=118.46  Aligned_cols=79  Identities=22%  Similarity=0.339  Sum_probs=69.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCc-eeEEEeecCCCCcceEEEEEcChHHHHHHH--hcC-CccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRS-HEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~-~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||. |..+.+.    +++||||+|.+.++|++|+  +++ ..|+|+.|+|+++
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a   80 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS   80 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEc
Confidence            456789999999999999999999999999 6656554    4799999999999999998  477 8999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++..+.
T Consensus        81 ~~~~~~~   87 (93)
T 2cqh_A           81 VSKKLRS   87 (93)
T ss_dssp             CCCCCCC
T ss_pred             cCccccC
Confidence            9876554

>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=99.77  E-value=2.1e-18  Score=121.50  Aligned_cols=81  Identities=20%  Similarity=0.246  Sum_probs=72.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHH---HHHhhcCceeEEEeecC--C---C-CcceEEEEEcChHHHHHHHh--cCCccCCe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLR---RYFSRFGRILDVYVPKR--T---G-HRGFGFVTFAEEVVADRVSR--RSHEICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~---~~f~~~G~v~~~~~~~~--~---~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~  166 (234)
                      ....++|||+|||+++++++|+   ++|++||.|..|.|+.+  +   + ++|||||+|.+.++|++||.  +++.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            4567899999999999999999   99999999999999832  2   2 56999999999999999984  78899999


Q ss_pred             EeEEEeCCCCCC
Q 026724          167 QVAIDSATPLDD  178 (234)
Q Consensus       167 ~i~v~~a~~~~~  178 (234)
                      .|+|.+|.++..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999998863

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.77  E-value=3.2e-19  Score=123.32  Aligned_cols=78  Identities=19%  Similarity=0.329  Sum_probs=71.5

Q ss_pred             CCCEEEEeCCCC------CCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCC-eE
Q 026724          100 IGKKIFVGRLPQ------EATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICG-QQ  167 (234)
Q Consensus       100 ~~~~l~v~nl~~------~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g-~~  167 (234)
                      .+++|||+|||+      ++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++||  +++..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467999999999      99999999999999999999998  5567 9999999999999999998  57889999 99


Q ss_pred             eEEEeCCCCC
Q 026724          168 VAIDSATPLD  177 (234)
Q Consensus       168 i~v~~a~~~~  177 (234)
                      |.|.++.+++
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999997653

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

Probab=99.77  E-value=2.9e-18  Score=121.96  Aligned_cols=77  Identities=27%  Similarity=0.445  Sum_probs=69.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+.  ++..|+|+.|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            5567899999999999999999999999999999998  4556 89999999999999999984  67899999999999


Q ss_pred             CC
Q 026724          173 AT  174 (234)
Q Consensus       173 a~  174 (234)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.77  E-value=1.9e-18  Score=121.47  Aligned_cols=77  Identities=26%  Similarity=0.541  Sum_probs=69.2

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||++ +++++|+++|++||.|..|.|     +++||||+|.+.++|++|+  +++..|+|+.|+|.++.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            335689999999999 999999999999999999999     4799999999999999998  37889999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      +....
T Consensus        99 ~~~~~  103 (110)
T 1wf1_A           99 EPKPD  103 (110)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            65543

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

Probab=99.77  E-value=3.7e-18  Score=118.08  Aligned_cols=76  Identities=30%  Similarity=0.579  Sum_probs=70.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      ++|||+|||+++|+++|+++|++||.|..|.++.+  +++||||+|.+.++|++|+.  ++..+.|+.|+|+++.++...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS--SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            47999999999999999999999999999999865  68999999999999999984  778999999999999987644

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.77  E-value=1.3e-18  Score=122.14  Aligned_cols=79  Identities=16%  Similarity=0.183  Sum_probs=68.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcC-ceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      .....+|||+|||+++++++|+++|++|| .|..+.|... .++|||||+|.+.++|++||  +++..|+|+.|+|+++.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~-~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR-DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC-SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC-CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            34568999999999999999999999999 8999988621 27899999999999999999  47889999999999997


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ...
T Consensus       104 ~~p  106 (111)
T 2jvr_A          104 NPP  106 (111)
T ss_dssp             C--
T ss_pred             CCC
Confidence            654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.77  E-value=2.8e-18  Score=123.14  Aligned_cols=80  Identities=23%  Similarity=0.369  Sum_probs=72.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~  175 (234)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|| ++++.|.|+.|+|.++++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            35799999999999999999999999999999998  3567 8999999999999999999 467799999999999987


Q ss_pred             CCCC
Q 026724          176 LDDA  179 (234)
Q Consensus       176 ~~~~  179 (234)
                      ....
T Consensus       115 ~~~~  118 (124)
T 2jwn_A          115 NMPG  118 (124)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            5543

>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=99.77  E-value=1.1e-18  Score=123.53  Aligned_cols=80  Identities=19%  Similarity=0.215  Sum_probs=72.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCce-eEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRI-LDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v-~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++|+++|+++|++||.| ..|.|+ ..++ ++|||||+|.+.++|++||. +++.|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVV   91 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEEC
Confidence            4567899999999999999999999999999 888888 3467 99999999999999999984 677999999999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      .++.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            8765

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.3e-18  Score=118.49  Aligned_cols=80  Identities=33%  Similarity=0.521  Sum_probs=69.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++|+   .|.++  +.++ +++||||+|.+.++|++||  ++++.|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            55688999999999999999999999884   44455  4456 8999999999999999998  478899999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      ++++.+..
T Consensus        89 a~~~~~~~   96 (102)
T 2fc8_A           89 AKPKGEGG   96 (102)
T ss_dssp             CCCCCSSS
T ss_pred             ecCCCCCC
Confidence            99877643

>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=99.77  E-value=3.6e-19  Score=125.96  Aligned_cols=81  Identities=19%  Similarity=0.388  Sum_probs=72.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      ...++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|| ++++.|.|+.|.|.++.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecC
Confidence            346799999999999999999999999999999998  4556 8999999999999999999 46789999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++..+
T Consensus       103 ~~~~~  107 (114)
T 2cq4_A          103 AEKNR  107 (114)
T ss_dssp             HHHHH
T ss_pred             CCccC
Confidence            76543

>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=99.77  E-value=1.4e-18  Score=119.54  Aligned_cols=80  Identities=15%  Similarity=0.174  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..+.++  +.++ ++|||||+|.+.++|++||.  ++..|.|+.|+|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4456899999999999999999999999999876665  5666 89999999999999999994  67799999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      +..+.
T Consensus        92 a~~~~   96 (98)
T 2cqp_A           92 GSGPS   96 (98)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            97643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=3.5e-18  Score=122.89  Aligned_cols=80  Identities=19%  Similarity=0.284  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHH----HHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+.+ ++ ++|||||+|.+.++|..|+  +++..|.|++|+|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~-~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL-SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC-CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc-CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            4457899999999999999876    6999999999988864 44 8999999999999999998  4788999999999


Q ss_pred             EeCCCCCC
Q 026724          171 DSATPLDD  178 (234)
Q Consensus       171 ~~a~~~~~  178 (234)
                      .|++++..
T Consensus       105 ~~a~~~~~  112 (127)
T 2a3j_A          105 TFSETPQS  112 (127)
T ss_dssp             EECCCCCH
T ss_pred             EEccCcch
Confidence            99987653

>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=99.77  E-value=2.9e-18  Score=119.86  Aligned_cols=77  Identities=23%  Similarity=0.369  Sum_probs=70.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+ ..++ +++||||+|.+.++|++|+.  ++..|.|+.|+|+++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            5568899999999999999999999999999999998 3366 89999999999999999984  788999999999998


Q ss_pred             C
Q 026724          174 T  174 (234)
Q Consensus       174 ~  174 (234)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.76  E-value=7.7e-18  Score=119.21  Aligned_cols=82  Identities=22%  Similarity=0.370  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCce----eEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRI----LDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v----~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v  170 (234)
                      ..+.++|||+|||+++|+++|+++|++||.|    ..+.+.  ++ ++|||||+|.+.++|++||.  ++..|.|+.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~--~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   99 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM--TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   99 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE--CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC--CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            4467899999999999999999999999998    444444  55 89999999999999999984  778999999999


Q ss_pred             EeCCCCCCCCC
Q 026724          171 DSATPLDDAGP  181 (234)
Q Consensus       171 ~~a~~~~~~~~  181 (234)
                      .++.++....+
T Consensus       100 ~~a~~~~~~~~  110 (115)
T 2cpx_A          100 EFGKNKKQRSS  110 (115)
T ss_dssp             EECCCCSCCCC
T ss_pred             EEccCCCCCCC
Confidence            99998876554

>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=99.76  E-value=9.2e-19  Score=120.98  Aligned_cols=79  Identities=20%  Similarity=0.421  Sum_probs=69.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeec---CCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~---~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++|| |.+|.|+.   .++ ++|||||+|.+.++|.+|| +++..|.|+.|+|++
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEe
Confidence            55679999999999999999999999999 99999983   367 8999999999999999999 467799999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      +.++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98764

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

Probab=99.76  E-value=1.7e-18  Score=129.17  Aligned_cols=77  Identities=18%  Similarity=0.346  Sum_probs=69.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcC--ceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..++|||+|||+++++++|+++|++||  .|.+|.|+  +.++ ++|||||+|.+.++|++||.  ++..|+|+.|.|.+
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  99999998  4577 99999999999999999984  78899999999999


Q ss_pred             CCCC
Q 026724          173 ATPL  176 (234)
Q Consensus       173 a~~~  176 (234)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.5e-18  Score=121.57  Aligned_cols=78  Identities=22%  Similarity=0.271  Sum_probs=69.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~  175 (234)
                      ....+|||+|||+++|+++|+++|++| .|..|.|+ ...+ ++|||||+|.+.++|++|| ++++.|.|+.|+|..+.+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            345799999999999999999999999 89999998 3346 9999999999999999999 477899999999998875


Q ss_pred             CC
Q 026724          176 LD  177 (234)
Q Consensus       176 ~~  177 (234)
                      +.
T Consensus        93 ~~   94 (109)
T 2dnn_A           93 RQ   94 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>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=99.76  E-value=6.2e-18  Score=113.16  Aligned_cols=74  Identities=24%  Similarity=0.431  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh---cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR---RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~---~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.+++.   ++||||+|.+.++|++|+.   ++..+.|+.|+|++++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~---kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR---QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG---GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC---CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            556789999999999999999999999999999999863   7999999999999999984   6679999999999985

>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=99.76  E-value=8.8e-19  Score=121.83  Aligned_cols=81  Identities=28%  Similarity=0.560  Sum_probs=73.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      ...++|||+|||+++++++|+++|++||.|..|.++  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            346899999999999999999999999999999988  4567 8999999999999999998  4778999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++...
T Consensus        86 ~~~~~~   91 (104)
T 1p1t_A           86 ASEKNK   91 (104)
T ss_dssp             TCTTHH
T ss_pred             CCccch
Confidence            987643

>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=99.76  E-value=1e-18  Score=114.14  Aligned_cols=71  Identities=35%  Similarity=0.681  Sum_probs=65.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      +|||+|||+++++++|+++|++||.|..|.++  +.++ ++|||||+|.+.++|++|+. +++.+.|+.|.|++|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999988  4556 89999999999999999995 677999999999875

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

Probab=99.76  E-value=1.7e-18  Score=118.76  Aligned_cols=78  Identities=22%  Similarity=0.470  Sum_probs=68.6

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ..+.++|||+|||+ ++++++|+++|++||.|..|.|.     ++||||+|.+.++|++|+.  ++..+.|+.|+|.++.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   81 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSS   81 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-----TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcC
Confidence            45688999999999 99999999999999999999994     7999999999999999984  7789999999999998


Q ss_pred             CCCCCC
Q 026724          175 PLDDAG  180 (234)
Q Consensus       175 ~~~~~~  180 (234)
                      ++....
T Consensus        82 ~~~~~~   87 (96)
T 2kvi_A           82 SNARPQ   87 (96)
T ss_dssp             CCCC--
T ss_pred             cCCCCC
Confidence            766543

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

Probab=99.76  E-value=4.6e-18  Score=119.07  Aligned_cols=77  Identities=21%  Similarity=0.392  Sum_probs=70.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.++     +|||||+|.+.++|++|+  +++..|+|+.|.|.++++
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  102 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL  102 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            5578999999999999999999999999999999996     699999999999999998  478899999999999988


Q ss_pred             CCCC
Q 026724          176 LDDA  179 (234)
Q Consensus       176 ~~~~  179 (234)
                      +..+
T Consensus       103 ~~~r  106 (108)
T 2jvo_A          103 PAKR  106 (108)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=1.9e-17  Score=118.87  Aligned_cols=83  Identities=22%  Similarity=0.336  Sum_probs=74.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ ++|||||+|.+.++|++|+.  ++..|.|+.|+|++|
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            5567899999999999999999999999999999998 3366 89999999999999999984  778999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .+.....
T Consensus       112 ~~~~~~~  118 (124)
T 2kt5_A          112 ASQIDLE  118 (124)
T ss_dssp             CCTTCCC
T ss_pred             CCCCCCC
Confidence            8866543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.75  E-value=1.8e-18  Score=114.79  Aligned_cols=70  Identities=23%  Similarity=0.460  Sum_probs=64.0

Q ss_pred             CCEEEEeCCCCCC------CHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCe-EeEE
Q 026724          101 GKKIFVGRLPQEA------TAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQ-QVAI  170 (234)
Q Consensus       101 ~~~l~v~nl~~~~------~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~-~i~v  170 (234)
                      +++|||+|||+.+      ++++|+++|++||.|.+|.+++.++ ++|||||+|.+.++|++|+.  ++..|.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3689999999999      7899999999999999999987777 99999999999999999994  77899999 8876

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

Probab=99.75  E-value=1.8e-17  Score=113.06  Aligned_cols=81  Identities=20%  Similarity=0.378  Sum_probs=68.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPL  176 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~~~  176 (234)
                      ....++|||+|||+++++++|+++|++||.|.+|.+.+.++.  ||||+|.+.++|++||. +++.|+|+.|.|+++.++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~--~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV--FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCC--EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCCS
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCc--EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCcC
Confidence            345679999999999999999999999999999832243323  99999999999999995 677999999999999876


Q ss_pred             CCCC
Q 026724          177 DDAG  180 (234)
Q Consensus       177 ~~~~  180 (234)
                      ....
T Consensus        83 ~~~~   86 (94)
T 2e5g_A           83 EFQS   86 (94)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.75  E-value=1.6e-18  Score=118.53  Aligned_cols=78  Identities=15%  Similarity=0.220  Sum_probs=67.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..+.++  +.++ +++||||+|.+.++|++||.  +++.|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            3346899999999999999999999999999877666  5566 89999999999999999984  78899999999999


Q ss_pred             CCC
Q 026724          173 ATP  175 (234)
Q Consensus       173 a~~  175 (234)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            864

>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=99.75  E-value=1.5e-17  Score=114.24  Aligned_cols=75  Identities=23%  Similarity=0.537  Sum_probs=68.7

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+ ++++++|+++|++||.|..|.+     ++|||||+|.+.++|.+|+  +++..+.|+.|+|++++
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   93 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSS   93 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            55689999999998 9999999999999999999999     4799999999999999998  47789999999999998


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ++.
T Consensus        94 ~~~   96 (97)
T 2xnq_A           94 SNA   96 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.1e-17  Score=114.83  Aligned_cols=79  Identities=19%  Similarity=0.411  Sum_probs=68.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|. +.++.. .+++||||+|.+.++|++|+  +++..|+|+.|.|+++.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~-~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ-GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC-CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            44578999999999999999999999999996 555521 16899999999999999998  478899999999999998


Q ss_pred             CCC
Q 026724          176 LDD  178 (234)
Q Consensus       176 ~~~  178 (234)
                      +..
T Consensus        94 ~~~   96 (97)
T 2e5j_A           94 QRD   96 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.5e-18  Score=116.20  Aligned_cols=76  Identities=20%  Similarity=0.385  Sum_probs=67.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+.  ++..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            457899999999999999999999999999999988  4566 89999999999999999984  677899998887765


Q ss_pred             C
Q 026724          174 T  174 (234)
Q Consensus       174 ~  174 (234)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.75  E-value=4.9e-18  Score=117.46  Aligned_cols=76  Identities=21%  Similarity=0.291  Sum_probs=69.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|.+|.+.+   +++||||+|.+.++|++|+  +++..|+|+.|+|.++++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP---EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec---CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            34568999999999999999999999999999999984   4899999999999999998  478899999999999987


Q ss_pred             C
Q 026724          176 L  176 (234)
Q Consensus       176 ~  176 (234)
                      +
T Consensus       101 ~  101 (101)
T 2la4_A          101 R  101 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=4.5e-17  Score=111.75  Aligned_cols=79  Identities=25%  Similarity=0.351  Sum_probs=70.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+||  ++++++|+++|++||.|..|.|.+   +++||||+|.+.++|++||.  ++..|.|+.|+|.++.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~---~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~   86 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP---PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   86 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSS
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC---CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCC
Confidence            456789999996  899999999999999999999864   58999999999999999984  67799999999999998


Q ss_pred             CCCCCC
Q 026724          176 LDDAGP  181 (234)
Q Consensus       176 ~~~~~~  181 (234)
                      +.....
T Consensus        87 ~~~~~~   92 (97)
T 1x5p_A           87 QPMLDS   92 (97)
T ss_dssp             CCCCCS
T ss_pred             CCCCCC
Confidence            765543

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

Probab=99.74  E-value=2e-18  Score=113.30  Aligned_cols=73  Identities=37%  Similarity=0.627  Sum_probs=65.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhc-CCccCCeEeEEEeCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRR-SHEICGQQVAIDSAT  174 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~a~  174 (234)
                      ++|||+|||+++++++|+++|++||.|..|.++  +.++ ++|||||+|.+.++|++|+.. .+.++|+.|.|++|.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~   77 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEecC
Confidence            479999999999999999999999999999998  3456 899999999999999999842 279999999999873

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.74  E-value=2.3e-18  Score=122.59  Aligned_cols=80  Identities=16%  Similarity=0.220  Sum_probs=70.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCc---eeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR---ILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~---v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~  171 (234)
                      ....++|||+|||+++|+++|+++|++||.   |..|+|+ ...+ ++|||||+|.+.++|++|| ++++.|.|+.|+|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            446789999999999999999999999999   8899888 3336 8999999999999999999 47779999999999


Q ss_pred             eCCCCC
Q 026724          172 SATPLD  177 (234)
Q Consensus       172 ~a~~~~  177 (234)
                      ++.+++
T Consensus        94 ~a~~~~   99 (118)
T 2db1_A           94 KSHRTE   99 (118)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987654

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

Probab=99.74  E-value=2.2e-17  Score=120.82  Aligned_cols=76  Identities=30%  Similarity=0.521  Sum_probs=69.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|+.  ++..|.|+.|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            5568999999999999999999999999999999998  3566 89999999999999999994  67799999999998


Q ss_pred             C
Q 026724          173 A  173 (234)
Q Consensus       173 a  173 (234)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=99.74  E-value=1.7e-18  Score=125.96  Aligned_cols=80  Identities=16%  Similarity=0.206  Sum_probs=70.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCc---eeEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR---ILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~---v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~  171 (234)
                      ....++|||+|||+++|+++|+++|++||.   |..|.|+ ...+ ++|||||+|.+.++|++||. ++..|+|+.|+|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF  120 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            456789999999999999999999999999   8889888 3336 89999999999999999994 6779999999999


Q ss_pred             eCCCCC
Q 026724          172 SATPLD  177 (234)
Q Consensus       172 ~a~~~~  177 (234)
                      ++.+++
T Consensus       121 ~a~~~e  126 (136)
T 2hgl_A          121 KSHRTE  126 (136)
T ss_dssp             ECCHHH
T ss_pred             ECChHH
Confidence            987543

>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=99.74  E-value=1.1e-17  Score=118.50  Aligned_cols=80  Identities=16%  Similarity=0.342  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+..++|||||+|.+.++|.+|+  +++..+.|+.|.|.++.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            446789999999999999999999999999999999854337999999999999999998  478899999999999986


Q ss_pred             CC
Q 026724          176 LD  177 (234)
Q Consensus       176 ~~  177 (234)
                      +.
T Consensus        85 ~~   86 (115)
T 3lqv_A           85 NR   86 (115)
T ss_dssp             HH
T ss_pred             Ch
Confidence            54

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-18  Score=120.53  Aligned_cols=81  Identities=20%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|.. .++  ..++ ++|||||+|.+.++|++|| ++++.|.|+.|+|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            345789999999999999999999999999877 333  4455 8999999999999999999 5777999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++..+
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            987654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.74  E-value=1.6e-18  Score=120.11  Aligned_cols=82  Identities=23%  Similarity=0.572  Sum_probs=73.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ ++|||||+|.+.++|++|+.+++.++|+.|.|.++.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCc
Confidence            3456899999999999999999999999999999998 3366 8999999999999999999988899999999999987


Q ss_pred             CCCC
Q 026724          176 LDDA  179 (234)
Q Consensus       176 ~~~~  179 (234)
                      +...
T Consensus        86 ~~~~   89 (102)
T 2xs2_A           86 KQNL   89 (102)
T ss_dssp             CC--
T ss_pred             Ccch
Confidence            6644

>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=99.74  E-value=1.4e-18  Score=124.78  Aligned_cols=80  Identities=20%  Similarity=0.347  Sum_probs=70.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEE-ee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVY-VP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~-~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++|+++|+++|++||.|..+. +. +.++ ++|||||+|.+.++|++|| ++++.|+|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            45678999999999999999999999999998743 33 5667 8999999999999999999 5777999999999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      .++.
T Consensus       102 ~~~~  105 (124)
T 1wel_A          102 TKKG  105 (124)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

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

Probab=99.60  E-value=1.2e-19  Score=128.95  Aligned_cols=82  Identities=26%  Similarity=0.372  Sum_probs=73.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE--------EEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~  164 (234)
                      ..+.++|||+|||+++++++|+++|++||.|..        |.|+  +.++ ++|||||+|.+.++|++|+.  ++..|.
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            446789999999999999999999999999998        7777  4566 89999999999999999984  778999


Q ss_pred             CeEeEEEeCCCCCCC
Q 026724          165 GQQVAIDSATPLDDA  179 (234)
Q Consensus       165 g~~i~v~~a~~~~~~  179 (234)
                      |+.|+|.++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999987654

>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=99.74  E-value=4.9e-18  Score=116.52  Aligned_cols=80  Identities=29%  Similarity=0.477  Sum_probs=71.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHH----HHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      ..++++|||+|||+++++++|+    ++|++||.|..|.+++ ++ ++|||||+|.+.++|.+|+  +++..+.|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH-HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc-CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            4567899999999999999999    9999999999999874 34 7899999999999999998  4788999999999


Q ss_pred             EeCCCCCC
Q 026724          171 DSATPLDD  178 (234)
Q Consensus       171 ~~a~~~~~  178 (234)
                      .++.++..
T Consensus        84 ~~a~~~~~   91 (97)
T 1nu4_A           84 QYAKTDSD   91 (97)
T ss_dssp             EECSSCCT
T ss_pred             EEccCCCc
Confidence            99998654

>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=99.74  E-value=2.6e-17  Score=116.35  Aligned_cols=79  Identities=16%  Similarity=0.356  Sum_probs=70.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH--hcCCcc--------CC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS--RRSHEI--------CG  165 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~--------~g  165 (234)
                      ....++|||+|||+++++++|+++|++||.|..|.|+ ..++ ++|||||+|.+.++|++|+  +++..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            4567899999999999999999999999999999998 3366 8999999999999999998  467777        68


Q ss_pred             eEeEEEeCCCC
Q 026724          166 QQVAIDSATPL  176 (234)
Q Consensus       166 ~~i~v~~a~~~  176 (234)
                      ++|.|.|+.|+
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999999865

>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=99.74  E-value=1.4e-17  Score=116.79  Aligned_cols=81  Identities=14%  Similarity=0.277  Sum_probs=70.0

Q ss_pred             CCCCCEEEE--eCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCcc-----CCeEe
Q 026724           98 QRIGKKIFV--GRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEI-----CGQQV  168 (234)
Q Consensus        98 ~~~~~~l~v--~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~-----~g~~i  168 (234)
                      ..++.+|||  +||++++++++|+++|++||.|.+|.|+.   .+|||||+|.+.++|++|+.  ++.+|     .+++|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~---~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l   98 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL   98 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEEC
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEE
Confidence            445789999  77999999999999999999999998875   37999999999999999984  67777     68999


Q ss_pred             EEEeCCCCCCCCC
Q 026724          169 AIDSATPLDDAGP  181 (234)
Q Consensus       169 ~v~~a~~~~~~~~  181 (234)
                      .|.+++..+...+
T Consensus        99 ~v~~a~~~p~~~~  111 (114)
T 2cq2_A           99 YLNFVEKVQWSGP  111 (114)
T ss_dssp             EEEEESCCCCSSC
T ss_pred             EEEecccCcccCC
Confidence            9999987665544

>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=99.74  E-value=3.6e-18  Score=122.41  Aligned_cols=78  Identities=21%  Similarity=0.345  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCcee--EEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL--DVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~  172 (234)
                      .....+|||+|||+++|+++|+++|++| .|.  .|.|+ ...+ ++|||||+|.+.++|++||. +...|.|+.|+|..
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            4457899999999999999999999999 566  88888 3336 99999999999999999995 56799999999998


Q ss_pred             CCCC
Q 026724          173 ATPL  176 (234)
Q Consensus       173 a~~~  176 (234)
                      +.++
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=6.2e-18  Score=115.80  Aligned_cols=79  Identities=20%  Similarity=0.339  Sum_probs=69.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..+   ..++ ++|||||+|.+.++|.+|+.  ++..|.|+.|.|.++.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            4467899999999999999999999999988766   4455 89999999999999999985  6779999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++...
T Consensus        90 ~~~~~   94 (96)
T 1fjc_A           90 EKGGT   94 (96)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.73  E-value=1.1e-17  Score=118.42  Aligned_cols=75  Identities=17%  Similarity=0.280  Sum_probs=63.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeE-----eEEE
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQ-----VAID  171 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~-----i~v~  171 (234)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+    +||||+|.+.++|++||  +++..|+|+.     |+|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~   89 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            45789999999999999999999999999999999754    99999999999999998  4778999988     7777


Q ss_pred             eCCCCC
Q 026724          172 SATPLD  177 (234)
Q Consensus       172 ~a~~~~  177 (234)
                      .+.++.
T Consensus        90 ~~~~~~   95 (115)
T 3beg_B           90 VDGPRS   95 (115)
T ss_dssp             ECC---
T ss_pred             cCCCCC
Confidence            776644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-18  Score=123.59  Aligned_cols=79  Identities=23%  Similarity=0.252  Sum_probs=69.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCce----eEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEE
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRI----LDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAID  171 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v----~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~  171 (234)
                      ....+|||+|||+++|+++|+++|++||.|    ..|.|+ ..++ ++|||||+|.+.++|++||. +++.|.++.|+|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            356899999999999999999999999975    578887 4466 89999999999999999995 6779999999999


Q ss_pred             eCCCCC
Q 026724          172 SATPLD  177 (234)
Q Consensus       172 ~a~~~~  177 (234)
                      .+.+++
T Consensus       101 ~a~~~e  106 (123)
T 2dha_A          101 RSTAAE  106 (123)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            886543

>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=99.73  E-value=2e-18  Score=116.88  Aligned_cols=77  Identities=30%  Similarity=0.615  Sum_probs=65.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~  176 (234)
                      ++|||+|||+++++++|+++|++||.|.+|.++  +.++ ++|||||+|.+.+ |.+|+.  ++..+.|+.|+|++|.+.
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            579999999999999999999999999999998  4456 8999999999999 999984  678999999999999886


Q ss_pred             CCC
Q 026724          177 DDA  179 (234)
Q Consensus       177 ~~~  179 (234)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            544

>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=99.73  E-value=7.8e-18  Score=118.50  Aligned_cols=75  Identities=21%  Similarity=0.232  Sum_probs=68.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..++|||+|||+++++++|+++|++||.|..|.|++   +++||||+|.+.++|++|+  +++..|.|+.|.|.|+....
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC---CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            467999999999999999999999999999999875   4799999999999999998  47889999999999997643

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.72  E-value=4e-18  Score=119.22  Aligned_cols=80  Identities=19%  Similarity=0.160  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCc---eeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR---ILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~---v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~  171 (234)
                      ....++|||+|||+++|+++|+++|++||.   |..|.|+ ...+ ++|||||+|.+.++|++|| ++++.|.|+.|+|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY   87 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEE
Confidence            456789999999999999999999999998   8899988 2236 9999999999999999999 46779999999999


Q ss_pred             eCCCCC
Q 026724          172 SATPLD  177 (234)
Q Consensus       172 ~a~~~~  177 (234)
                      ++.+++
T Consensus        88 ~a~~~~   93 (107)
T 2lmi_A           88 EINNED   93 (107)
T ss_dssp             ECCHHH
T ss_pred             ECCHHH
Confidence            997654

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

Probab=99.72  E-value=1.7e-17  Score=117.37  Aligned_cols=78  Identities=26%  Similarity=0.452  Sum_probs=67.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC---C-CcceEEEEEcChHHHHHHHhcCCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT---G-HRGFGFVTFAEEVVADRVSRRSHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~---~-~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~  171 (234)
                      ....++|||+|||+++++++|+++|++||.|. +.++  +.+   + ++|||||+|.+.++|++||...+.++|+.|.+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~   83 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCV   83 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEec
Confidence            34578999999999999999999999999999 7666  333   5 899999999999999999987778899888887


Q ss_pred             eCCCC
Q 026724          172 SATPL  176 (234)
Q Consensus       172 ~a~~~  176 (234)
                      .+.+.
T Consensus        84 ~~~~~   88 (114)
T 2dnl_A           84 SSPTI   88 (114)
T ss_dssp             CCSSS
T ss_pred             cCCCc
Confidence            66543

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

Probab=99.71  E-value=8e-17  Score=110.21  Aligned_cols=79  Identities=11%  Similarity=0.114  Sum_probs=68.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEE-eecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVY-VPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~-~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|..|+ |+.+. ..+.|||+|.+.++|.+|+  +++..|.|+.|.|+++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~-~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS-SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            44578999999999999999999999999999995 66332 2344999999999999998  47889999999999999


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ++.
T Consensus        91 ~~~   93 (96)
T 2e44_A           91 DEM   93 (96)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            884

>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=99.71  E-value=4.8e-17  Score=120.93  Aligned_cols=78  Identities=21%  Similarity=0.275  Sum_probs=68.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCC--eEeEEEeCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICG--QQVAIDSAT  174 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g--~~i~v~~a~  174 (234)
                      ....+|||+||++.+|+++|+++|++||.|++|.|.... +++||||+|.+.++|++|+.  ++..|.+  +.|+|+|++
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~-~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS-SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            345679999999999999999999999999999987321 57899999999999999984  7778865  999999999


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ++.
T Consensus       123 ~~~  125 (164)
T 1sjr_A          123 LTS  125 (164)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            874

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.70  E-value=8.2e-17  Score=115.42  Aligned_cols=76  Identities=22%  Similarity=0.336  Sum_probs=67.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcce-EEEEEcChHHHHHHH--hcCCccCC--eEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGF-GFVTFAEEVVADRVS--RRSHEICG--QQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~-afV~f~~~~~a~~A~--~~~~~~~g--~~i~v~~a~  174 (234)
                      ...+|||+||++.+|+++|+++|++||.|.+|.++..  .++| |||+|.+.++|++|+  +++..|.+  +.|+|+|++
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~--~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE--TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECS
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC--CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecC
Confidence            4467889999999999999999999999999988743  3688 999999999999998  57889988  899999999


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ++.
T Consensus       105 ~~~  107 (130)
T 3zzy_A          105 LTS  107 (130)
T ss_dssp             CSS
T ss_pred             CCc
Confidence            864

>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=99.70  E-value=2.6e-17  Score=121.06  Aligned_cols=82  Identities=17%  Similarity=0.306  Sum_probs=69.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEE--------EeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV--------YVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~--------~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~  166 (234)
                      ..+.++|||+|||+++|+++|+++|++||.|..|        .+ ..++ ++|||||+|.+.++|.+||  +++..|.|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            4467899999999999999999999999998764        22 2345 8999999999999999998  478899999


Q ss_pred             EeEEEeCCCCCCCC
Q 026724          167 QVAIDSATPLDDAG  180 (234)
Q Consensus       167 ~i~v~~a~~~~~~~  180 (234)
                      .|.|.++++..++.
T Consensus       121 ~l~V~~a~~~~~~~  134 (143)
T 3egn_A          121 PMVVQFARSARPKQ  134 (143)
T ss_dssp             ECEEEECCCSCC--
T ss_pred             EEEEEECCCCCCcc
Confidence            99999998765443

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

Probab=99.69  E-value=8.1e-17  Score=122.53  Aligned_cols=80  Identities=21%  Similarity=0.338  Sum_probs=72.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+.+++++|+++|++||.|+.|.|+ ..++ ++|||||+|.+.++|++||.  ++..|.|+.|+|.++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            5567899999999999999999999999999999998 3366 89999999999999999985  778999999999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      .+..
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.69  E-value=3.6e-16  Score=111.51  Aligned_cols=73  Identities=18%  Similarity=0.257  Sum_probs=65.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcce-EEEEEcChHHHHHHH--hcCCccCC--eEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGF-GFVTFAEEVVADRVS--RRSHEICG--QQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~-afV~f~~~~~a~~A~--~~~~~~~g--~~i~v~~a~~~  176 (234)
                      ..|||+||++.+++++|+++|++||.|.+|.|...   .|| |||+|.+.++|..|+  +++..|.|  +.|+|.+|+++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~---~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES---SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCC
Confidence            45789999999999999999999999999998743   386 999999999999998  47889987  69999999987


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      .
T Consensus       103 ~  103 (124)
T 2e5i_A          103 R  103 (124)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.8e-16  Score=105.95  Aligned_cols=74  Identities=18%  Similarity=0.345  Sum_probs=64.2

Q ss_pred             CCCCE-EEEeCCCCCCCHHH----HHHHHhhc-CceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724           99 RIGKK-IFVGRLPQEATAED----LRRYFSRF-GRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus        99 ~~~~~-l~v~nl~~~~~~~~----l~~~f~~~-G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      .++.+ |||+|||+.+++++    |+++|++| |+|.+|     +  .|+|||+|.+.++|.+|+  +++..|.|++|+|
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-----t--gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-----T--GCSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-----C--TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-----e--cCEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            34555 99999999999988    55899999 599888     2  399999999999999998  4788999999999


Q ss_pred             EeCCCCCCC
Q 026724          171 DSATPLDDA  179 (234)
Q Consensus       171 ~~a~~~~~~  179 (234)
                      .+|+.+..-
T Consensus        79 ~~A~~~sd~   87 (96)
T 2diu_A           79 SFTPKNREL   87 (96)
T ss_dssp             ESSCCSCCC
T ss_pred             EecCCCcce
Confidence            999987654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=1.5e-16  Score=124.62  Aligned_cols=80  Identities=26%  Similarity=0.282  Sum_probs=70.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+  +.++ ++|||||+|.+.++|++||.  ++..+.|+.|+|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            3457899999999999999999999999999999998  4566 89999999999999999984  67799999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            87654

>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=99.68  E-value=1.6e-16  Score=122.33  Aligned_cols=82  Identities=35%  Similarity=0.547  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|.+||. +++.+.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecc
Confidence            4567899999999999999999999999999999998  4466 89999999999999999995 677999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++...
T Consensus        90 ~~~~~~   95 (196)
T 1l3k_A           90 VSREDS   95 (196)
T ss_dssp             CC----
T ss_pred             cCcccc
Confidence            876543

>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=99.68  E-value=1.3e-16  Score=107.52  Aligned_cols=74  Identities=16%  Similarity=0.282  Sum_probs=66.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..++|||+|||+++++++|+++|++| .|.+|.+.+   ++|||||+|.+.++|++|+  +++..+.|+.|+|+++....
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~---~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDR---NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEG---GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeC---CCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            46899999999999999999999999 999998863   6899999999999999998  47789999999999996543

>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=99.68  E-value=1.1e-16  Score=120.17  Aligned_cols=78  Identities=33%  Similarity=0.657  Sum_probs=71.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~~~  176 (234)
                      ++++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|.+|+.+++.++|+.|.|.++.++
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccch
Confidence            36799999999999999999999999999999998  3467 99999999999999999999889999999999998765


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      .
T Consensus        82 ~   82 (167)
T 2cjk_A           82 D   82 (167)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.67  E-value=4.3e-16  Score=116.98  Aligned_cols=80  Identities=24%  Similarity=0.416  Sum_probs=72.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      +.++|||+|||+++++++|+++|++||.|.+|.++  +.++ ++|||||+|.+.++|.+|+  +++..+.|+.|.|.++.
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            46899999999999999999999999999999998  4567 8999999999999999998  47889999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++...
T Consensus        82 ~~~~~   86 (168)
T 1b7f_A           82 PGGES   86 (168)
T ss_dssp             CCSST
T ss_pred             CCccc
Confidence            76643

>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=99.67  E-value=2.8e-16  Score=105.41  Aligned_cols=71  Identities=21%  Similarity=0.407  Sum_probs=64.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhc----C-------ceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCe
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRF----G-------RILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQ  166 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~----G-------~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~  166 (234)
                      .+.++|||+|||+++++++|+++|++|    |       .|.++.+.++   +|||||+|.+.++|.+|+ +++..+.|+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~---kg~afV~f~~~~~a~~A~~l~g~~~~g~   80 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD---KNFAFLEFRSVDETTQAMAFDGIIFQGQ   80 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS---SSEEEEEESSHHHHHHHGGGTTCEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC---CcEEEEEcCCHHHHHHHHhcCCCEECCe
Confidence            457899999999999999999999999    8       8999988754   799999999999999998 467799999


Q ss_pred             EeEEEe
Q 026724          167 QVAIDS  172 (234)
Q Consensus       167 ~i~v~~  172 (234)
                      .|+|+.
T Consensus        81 ~l~V~r   86 (87)
T 2hzc_A           81 SLKIRR   86 (87)
T ss_dssp             ECEEEC
T ss_pred             EEEEeC
Confidence            999974

>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=99.67  E-value=4.1e-16  Score=121.45  Aligned_cols=76  Identities=17%  Similarity=0.228  Sum_probs=69.6

Q ss_pred             CCCEEEEeCCC-CCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724          100 IGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       100 ~~~~l~v~nl~-~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      ++++|||+||| +.+++++|+++|++||.|.+|+|+++  ++|||||+|.+.++|++||  +++..|.|+.|+|.+++.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP   80 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCC
Confidence            46899999999 89999999999999999999999854  5899999999999999998  5888999999999999754


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      .
T Consensus        81 ~   81 (205)
T 3tyt_A           81 A   81 (205)
T ss_dssp             C
T ss_pred             c
Confidence            3

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.66  E-value=5.3e-16  Score=116.20  Aligned_cols=78  Identities=26%  Similarity=0.449  Sum_probs=71.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      +++|||+|||+++++++|+++|++||.|.+|.++  +.++ ++|||||+|.+.++|.+|+  +++..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            5799999999999999999999999999999998  3366 8899999999999999998  478899999999999987


Q ss_pred             CCC
Q 026724          176 LDD  178 (234)
Q Consensus       176 ~~~  178 (234)
                      ...
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.7e-16  Score=112.16  Aligned_cols=73  Identities=15%  Similarity=0.136  Sum_probs=64.1

Q ss_pred             CEEEEeCC----CCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcC----hHH----HHHHHh----cCCc
Q 026724          102 KKIFVGRL----PQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAE----EVV----ADRVSR----RSHE  162 (234)
Q Consensus       102 ~~l~v~nl----~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~----~~~----a~~A~~----~~~~  162 (234)
                      .+|||+||    |+.+++++|+++|++||+|.+|.++  +.|+ ++|||||+|.+    +++    |.+|+.    ++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999998  8888 99999999996    322    677765    6779


Q ss_pred             cCCeEeEEEeCC
Q 026724          163 ICGQQVAIDSAT  174 (234)
Q Consensus       163 ~~g~~i~v~~a~  174 (234)
                      |+|+.|+|.+..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999865

>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=99.64  E-value=9.4e-16  Score=118.23  Aligned_cols=77  Identities=16%  Similarity=0.314  Sum_probs=68.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~~~  176 (234)
                      ..++|||+|||+++++++|+++|++||.|..|+|+ ..++ ++|||||+|.+.++|.+|+. ..+.++|+.|.|.++..-
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            35799999999999999999999999999999998 3346 89999999999999999995 456999999999988753

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=1.5e-15  Score=113.61  Aligned_cols=77  Identities=21%  Similarity=0.351  Sum_probs=69.3

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ++|||+|||+++|+++|+++|++||.|.+|.++ ..++ ++|||||+|.+.++|.+|+  +++..+.|+.|.|.++.+..
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            489999999999999999999999999999998 3334 8999999999999999998  47889999999999998765


Q ss_pred             C
Q 026724          178 D  178 (234)
Q Consensus       178 ~  178 (234)
                      .
T Consensus        81 ~   81 (166)
T 3md3_A           81 Q   81 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-14  Score=99.87  Aligned_cols=78  Identities=14%  Similarity=0.204  Sum_probs=66.6

Q ss_pred             CCEEEEeCCC-------CCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeC
Q 026724          101 GKKIFVGRLP-------QEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSA  173 (234)
Q Consensus       101 ~~~l~v~nl~-------~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a  173 (234)
                      ..+|-|.-..       .++++++|+++|++||.|.+|.|+..  ++|||||+|.+.++|++||..++.+.+++|+|+|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~--~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSK--KPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESS--SSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccC--CCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEc
Confidence            5567776543       45899999999999999999999832  79999999999999999998888889999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++....
T Consensus        88 ~~~~~~~   94 (100)
T 2d9o_A           88 EGQPQDA   94 (100)
T ss_dssp             SCCCCCC
T ss_pred             cCCCCCC
Confidence            8876543

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

Probab=99.61  E-value=1.5e-15  Score=119.97  Aligned_cols=78  Identities=22%  Similarity=0.344  Sum_probs=67.7

Q ss_pred             CCCCCEEEEeCCCCCC---------CHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCcc---
Q 026724           98 QRIGKKIFVGRLPQEA---------TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEI---  163 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~---------~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~---  163 (234)
                      ....++|||+||+..+         ++++|+++|++||.|++|+|+.   ++|||||+|.+.++|+.|+  +++..|   
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~---~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~  207 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE---SKNCGFVKFKYQANAEFAKEAMSNQTLLLP  207 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHHHTTCCCCCT
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC---CCCEEEEEeCCHHHHHHHHHHhCCCEEecc
Confidence            5578999999999998         7999999999999999999986   3899999999999999998  467777   


Q ss_pred             ---------CCeEeEEEeCCCCCC
Q 026724          164 ---------CGQQVAIDSATPLDD  178 (234)
Q Consensus       164 ---------~g~~i~v~~a~~~~~  178 (234)
                               .|+.|.|+||.+...
T Consensus       208 ~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          208 SDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccCCCCEEEEEEccCCCC
Confidence                     899999999987654

>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=99.60  E-value=4.7e-15  Score=120.76  Aligned_cols=79  Identities=27%  Similarity=0.450  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHH----HHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      ..+.++|||+|||+++++++|+    ++|++||.|.+|.|++ ++ ++|||||+|.+.++|.+||  +++..|.|+.|+|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC-CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            5568999999999999999977    8999999999999886 44 8999999999999999998  4778999999999


Q ss_pred             EeCCCCC
Q 026724          171 DSATPLD  177 (234)
Q Consensus       171 ~~a~~~~  177 (234)
                      .++..+.
T Consensus        85 ~~a~~~~   91 (282)
T 3pgw_A           85 QYAKTDS   91 (282)
T ss_pred             EEeccCc
Confidence            9997655

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

Probab=99.60  E-value=4.4e-15  Score=115.99  Aligned_cols=78  Identities=23%  Similarity=0.441  Sum_probs=68.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|.+|+.  ++..|.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            46799999999999999999999999999999998  3356 89999999999999999984  7889999999999887


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ...
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            654

>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=99.60  E-value=1.6e-14  Score=101.57  Aligned_cols=82  Identities=21%  Similarity=0.242  Sum_probs=68.7

Q ss_pred             CCCCCEEEEeCCCCCCC-----------HHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccC
Q 026724           98 QRIGKKIFVGRLPQEAT-----------AEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~-----------~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~  164 (234)
                      ..++++|+|.||....+           +++|+++|++||.|..|.|.. ..++|||||+|.+.++|++|+  +++..|+
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~-~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD-RHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEET-TCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEec-CCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            55689999999954432           689999999999999997652 227999999999999999998  4778999


Q ss_pred             CeEeEEEeCCCCCCCC
Q 026724          165 GQQVAIDSATPLDDAG  180 (234)
Q Consensus       165 g~~i~v~~a~~~~~~~  180 (234)
                      |+.|+|.++.++....
T Consensus        91 gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           91 GRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             TEECEEEECCSCCCSS
T ss_pred             CcEEEEEEeCCCCCcc
Confidence            9999999998876543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.58  E-value=1.2e-14  Score=100.98  Aligned_cols=78  Identities=10%  Similarity=0.057  Sum_probs=67.0

Q ss_pred             CCCCCEEEEeCCCC-----CCCHHHHHHHHhhcCceeEEEeecC---CC-CcceEEEEEcChHHHHHHH--hcCCccCCe
Q 026724           98 QRIGKKIFVGRLPQ-----EATAEDLRRYFSRFGRILDVYVPKR---TG-HRGFGFVTFAEEVVADRVS--RRSHEICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~-----~~~~~~l~~~f~~~G~v~~~~~~~~---~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~  166 (234)
                      ..++++|+|.||..     +.++++|+++|++||.|.+|.|+.+   ++ ++||+||+|.+.++|.+|+  +++..++|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34678999999963     2378999999999999999999832   34 8999999999999999998  588899999


Q ss_pred             EeEEEeCCC
Q 026724          167 QVAIDSATP  175 (234)
Q Consensus       167 ~i~v~~a~~  175 (234)
                      .|.|.++.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999865

>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=99.58  E-value=1e-14  Score=115.43  Aligned_cols=78  Identities=17%  Similarity=0.228  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|.|+.+  .+|||||+|.+.++|++|+  +++..|.|+.|.|.++.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~--~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  108 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT--TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEEC--CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            45678999999999 9999999999999999999999855  3799999999999999998  47889999999999998


Q ss_pred             CCC
Q 026724          175 PLD  177 (234)
Q Consensus       175 ~~~  177 (234)
                      ++.
T Consensus       109 ~~~  111 (229)
T 2adc_A          109 HQN  111 (229)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            764

>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=99.56  E-value=2.6e-15  Score=113.60  Aligned_cols=82  Identities=21%  Similarity=0.358  Sum_probs=70.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.+..+.+. ..++ ++|||||+|.+.++|.+|+ +++..|.|+.|.|.++.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCC
Confidence            5568899999999999999999999999987663333 3445 8999999999999999999 47779999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++...
T Consensus        90 ~~~~~   94 (175)
T 1fje_B           90 GRDSK   94 (175)
T ss_dssp             CSSCS
T ss_pred             Ccccc
Confidence            76543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.54  E-value=1.8e-14  Score=111.23  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=69.4

Q ss_pred             CCCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724          100 IGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       100 ~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      .+++|||+|||+ ++++++|+++|++||.|.+|.++.+  .+|||||+|.+.++|.+|+  +++..+.|+.|.|.++.+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTT--CSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            368999999999 9999999999999999999999855  3799999999999999998  4788999999999999876


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      .
T Consensus        80 ~   80 (198)
T 1qm9_A           80 N   80 (198)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.54  E-value=3.4e-14  Score=114.59  Aligned_cols=75  Identities=29%  Similarity=0.572  Sum_probs=68.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++|+++|+++|++||.|..|.|.+.   +|||||+|.+.++|.+|+  +++..|.|+.|.|.++.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD---RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC---CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            456789999999999999999999999999999999753   799999999999999998  478899999999999875

>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=99.53  E-value=2.9e-14  Score=107.51  Aligned_cols=79  Identities=23%  Similarity=0.449  Sum_probs=66.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC---CCcceEEEEEcChHHHHHHHh--cCCccC---CeEeE
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT---GHRGFGFVTFAEEVVADRVSR--RSHEIC---GQQVA  169 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~---~~~g~afV~f~~~~~a~~A~~--~~~~~~---g~~i~  169 (234)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+  +.+   .++|||||+|.+.++|++|+.  ++..+.   ++.+.
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            36799999999999999999999999999999998  333   278999999999999999984  554444   67888


Q ss_pred             EEeCCCCCC
Q 026724          170 IDSATPLDD  178 (234)
Q Consensus       170 v~~a~~~~~  178 (234)
                      +.++.+...
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            888776554

>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=99.53  E-value=5.6e-14  Score=105.78  Aligned_cols=76  Identities=20%  Similarity=0.386  Sum_probs=66.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc----C-------ceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeE
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRF----G-------RILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQ  167 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~----G-------~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~  167 (234)
                      +.++|||+|||+++|+++|+++|++|    |       .|.++.+.+   ++|||||+|.+.++|.+|+ ++++.+.|+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~---~~g~afV~f~~~~~A~~A~~~~~~~~~g~~   79 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---DKNFAFLEFRSVDETTQAMAFDGIIFQGQS   79 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET---TTTEEEEEESSHHHHHHHGGGTTCEETTEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC---CCCEEEEEeCCHHHHHHHHHhCCcEecCce
Confidence            36799999999999999999999999    6       677777764   4899999999999999998 4678999999


Q ss_pred             eEEEeCCCCCC
Q 026724          168 VAIDSATPLDD  178 (234)
Q Consensus       168 i~v~~a~~~~~  178 (234)
                      |.|.++.+...
T Consensus        80 i~v~~~~~~~~   90 (172)
T 2g4b_A           80 LKIRRPHDYQP   90 (172)
T ss_dssp             CEEECCSSCCC
T ss_pred             eeecCCcccCC
Confidence            99999876543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.52  E-value=8.6e-14  Score=107.14  Aligned_cols=76  Identities=20%  Similarity=0.405  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc----C-------ceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeE
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRF----G-------RILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQ  167 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~----G-------~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~  167 (234)
                      ..++|||+|||+++|+++|+++|++|    |       .|.++.+.+   ++|||||+|.+.++|++|| +++..|.|+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~---~~g~afV~F~~~~~A~~Al~l~g~~~~g~~   79 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---DKNFAFLEFRSVDETTQAMAFDGIIFQGQS   79 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEET---TTTEEEEEESCSHHHHHHGGGTTEEETTEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecC---CCCEEEEEeCCHHHHHHHHHhcCCEEcCce
Confidence            46899999999999999999999999    5       566666544   5899999999999999999 4677999999


Q ss_pred             eEEEeCCCCCC
Q 026724          168 VAIDSATPLDD  178 (234)
Q Consensus       168 i~v~~a~~~~~  178 (234)
                      |.|.++.+...
T Consensus        80 i~v~~~~~~~~   90 (198)
T 2yh0_A           80 LKIRRPHDYQP   90 (198)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999887643

>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=99.47  E-value=2e-14  Score=101.61  Aligned_cols=74  Identities=16%  Similarity=0.332  Sum_probs=39.4

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      ++|+  +.+||||||+|.+.++|++||+  +++.|+|++|.|.++.++........                        
T Consensus        38 ~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~------------------------   91 (115)
T 4f25_A           38 VCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG------------------------   91 (115)
T ss_dssp             EEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC------------------------------
T ss_pred             eecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccccccc------------------------
Confidence            4554  4589999999999999999994  78899999999999876543321110                        


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAED  117 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  117 (234)
                                      .......+|||+|||+++|++.
T Consensus        92 ----------------~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           92 ----------------ARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             --------------------------------------
T ss_pred             ----------------cccCCCCceEeCCCCCCccccc
Confidence                            0023456799999999999864

>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=99.45  E-value=3.5e-13  Score=93.48  Aligned_cols=77  Identities=18%  Similarity=0.305  Sum_probs=64.7

Q ss_pred             CCCCEEEEeCC--CCCC--------CHHHHHHHHhhcCceeEEEeecCC----C-CcceEEEEEcChHHHHHHH--hcCC
Q 026724           99 RIGKKIFVGRL--PQEA--------TAEDLRRYFSRFGRILDVYVPKRT----G-HRGFGFVTFAEEVVADRVS--RRSH  161 (234)
Q Consensus        99 ~~~~~l~v~nl--~~~~--------~~~~l~~~f~~~G~v~~~~~~~~~----~-~~g~afV~f~~~~~a~~A~--~~~~  161 (234)
                      .+++.|.|.|+  |..+        .+++|+++|++||.|.+|.|+++.    + ++||+||+|.+.++|.+|+  +++.
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            35789999998  3343        247899999999999999998332    3 6899999999999999998  5888


Q ss_pred             ccCCeEeEEEeCCC
Q 026724          162 EICGQQVAIDSATP  175 (234)
Q Consensus       162 ~~~g~~i~v~~a~~  175 (234)
                      .++||.|+|.++.+
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            99999999998754

>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=99.43  E-value=5e-14  Score=97.67  Aligned_cols=68  Identities=15%  Similarity=0.270  Sum_probs=58.5

Q ss_pred             EeCCCCCCCHHHHHHHH------------hhcCceeEEEeecC-CC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeE
Q 026724          106 VGRLPQEATAEDLRRYF------------SRFGRILDVYVPKR-TG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVA  169 (234)
Q Consensus       106 v~nl~~~~~~~~l~~~f------------~~~G~v~~~~~~~~-~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~  169 (234)
                      +.+|++.+++++|+++|            ++||.|.+|.|+++ ++ ++|||||+|.+.++|.+|+  +++..++|+.|.
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            56788888888777666            99999999999933 34 8999999999999999998  478899999999


Q ss_pred             EEeC
Q 026724          170 IDSA  173 (234)
Q Consensus       170 v~~a  173 (234)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.42  E-value=5.4e-13  Score=110.82  Aligned_cols=74  Identities=14%  Similarity=0.286  Sum_probs=62.9

Q ss_pred             CCCCCEEEEeC--CCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCcc---CCe--Ee
Q 026724           98 QRIGKKIFVGR--LPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEI---CGQ--QV  168 (234)
Q Consensus        98 ~~~~~~l~v~n--l~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~---~g~--~i  168 (234)
                      ..++.+|||+|  |++.+|+++|+++|++||+|.+|.+..   +||||||+|++.++|++|+.  ++.++   .|+  .|
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~---~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~l   91 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL   91 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT---TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEEC
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEE
Confidence            56788999999  588999999999999999999988765   48999999999999999984  66655   345  67


Q ss_pred             EEEeCC
Q 026724          169 AIDSAT  174 (234)
Q Consensus       169 ~v~~a~  174 (234)
                      .|.++.
T Consensus        92 y~~~~~   97 (345)
T 3tht_A           92 YLNFVE   97 (345)
T ss_dssp             EEEECS
T ss_pred             EEEEee
Confidence            888874

>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=99.39  E-value=1.3e-12  Score=92.32  Aligned_cols=76  Identities=11%  Similarity=0.144  Sum_probs=64.4

Q ss_pred             CCCEEEEeCCCC--C---CCHHHHHHHHhhcCceeEEEeec--C----CC-CcceEEEEEcChHHHHHHH--hcCCccCC
Q 026724          100 IGKKIFVGRLPQ--E---ATAEDLRRYFSRFGRILDVYVPK--R----TG-HRGFGFVTFAEEVVADRVS--RRSHEICG  165 (234)
Q Consensus       100 ~~~~l~v~nl~~--~---~~~~~l~~~f~~~G~v~~~~~~~--~----~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g  165 (234)
                      ++++|+|.|+-.  +   -.++||++.|++||.|.+|.|++  .    ++ ++||+||+|.+.++|.+|+  +++..++|
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            578999999932  2   24789999999999999999982  2    34 6799999999999999998  58889999


Q ss_pred             eEeEEEeCCC
Q 026724          166 QQVAIDSATP  175 (234)
Q Consensus       166 ~~i~v~~a~~  175 (234)
                      |.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998753

>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=99.33  E-value=9.6e-12  Score=87.32  Aligned_cols=77  Identities=12%  Similarity=0.163  Sum_probs=64.1

Q ss_pred             CCCCCEEEEeCCCCCC----------CHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCC
Q 026724           98 QRIGKKIFVGRLPQEA----------TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICG  165 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~----------~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g  165 (234)
                      ..+++.|.|.|+=...          .+++|+++|++||.|.+|.|.+++ .+||+||+|.+.++|.+|+  +++..++|
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~-~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS-AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3467889999983221          246889999999999999997543 5899999999999999998  58889999


Q ss_pred             eEeEEEeCCC
Q 026724          166 QQVAIDSATP  175 (234)
Q Consensus       166 ~~i~v~~a~~  175 (234)
                      +.|.|.++..
T Consensus        83 R~i~v~~~~~   92 (114)
T 3s6e_A           83 KMITAAYVPL   92 (114)
T ss_dssp             EECEEEEECH
T ss_pred             EEEEEEEEcH
Confidence            9999999853

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.32  E-value=2.8e-12  Score=86.63  Aligned_cols=49  Identities=20%  Similarity=0.415  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhc---CceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVD---THELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~---~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+++||||||+|.+.++|++||+.   ...|+|++|.|.++.++..
T Consensus        34 i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~   85 (91)
T 2lxi_A           34 LMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPK   85 (91)
T ss_dssp             SSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCC
T ss_pred             EEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCC
Confidence            579999999999999999999999999953   4479999999999987654

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

Probab=99.27  E-value=4.4e-12  Score=86.27  Aligned_cols=46  Identities=28%  Similarity=0.497  Sum_probs=41.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cC----ceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DT----HELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~----~~i~gr~i~v~~a~~   46 (234)
                      |++|+.|++|||||||+|.+.++|++||+  ++    +.|+||+|.|++|.+
T Consensus        43 i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           43 LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             EEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            57999999999999999999999999994  43    369999999999864

>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=99.25  E-value=4.4e-12  Score=87.00  Aligned_cols=46  Identities=24%  Similarity=0.420  Sum_probs=42.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.||++||||||+|.+.++|++||+  ++..|.|++|+|.+|.|
T Consensus        51 i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           51 LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             EEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             eeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46899999999999999999999999994  78899999999999865

>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=99.20  E-value=2.3e-11  Score=83.86  Aligned_cols=51  Identities=20%  Similarity=0.352  Sum_probs=46.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDF   51 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~~~   51 (234)
                      |++|+.|+++||||||+|.+.++|++||.+++.|+|+.|.|.++.++....
T Consensus        47 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cqg_A           47 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQD   97 (103)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCCCC
T ss_pred             EEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCCCCcCC
Confidence            467889999999999999999999999998999999999999998876544

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.20  E-value=1.3e-10  Score=81.77  Aligned_cols=74  Identities=19%  Similarity=0.213  Sum_probs=63.6

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcC-hHHHHHHHhc----CCccCCeEeEEE
Q 026724           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAE-EVVADRVSRR----SHEICGQQVAID  171 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~-~~~a~~A~~~----~~~~~g~~i~v~  171 (234)
                      ..+.+.|||+||+++ +++++|+++|++||.|..|.+..+   .-.|||.|.+ .++|..|+..    +..|++..++++
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g---~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG---AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT---CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecC---CCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            567899999999999 999999999999999999999854   2479999999 7888888742    558899888887


Q ss_pred             eCC
Q 026724          172 SAT  174 (234)
Q Consensus       172 ~a~  174 (234)
                      ...
T Consensus        92 vL~   94 (121)
T 1owx_A           92 VLE   94 (121)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=1.4e-10  Score=76.77  Aligned_cols=75  Identities=20%  Similarity=0.282  Sum_probs=62.3

Q ss_pred             CCCCEEEEeCCC----CCCCH----HHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeEeE
Q 026724           99 RIGKKIFVGRLP----QEATA----EDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQVA  169 (234)
Q Consensus        99 ~~~~~l~v~nl~----~~~~~----~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~  169 (234)
                      ++..+|+|.-++    .++-.    .+|.+.|++||.|..++++.+     .+||+|.+.++|.+|| +++..++|+.|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-----~~fVtF~d~~sAlaAi~mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-----KMWVTFLEGSSALNVLSLNGKELLNRTIT   79 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-----SEEEEESSHHHHHHGGGGTTCEETTEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-----CEEEEECChHHHHHHHhcCCeEeCCeEEE
Confidence            456788888776    23333    678999999999999999754     4899999999999999 588899999999


Q ss_pred             EEeCCCCCC
Q 026724          170 IDSATPLDD  178 (234)
Q Consensus       170 v~~a~~~~~  178 (234)
                      |+++.|.-.
T Consensus        80 V~lkt~dW~   88 (91)
T 2dnr_A           80 IALKSPSGP   88 (91)
T ss_dssp             EEECCCSSC
T ss_pred             EEeCCCCcc
Confidence            999987643

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

Probab=99.18  E-value=1.9e-11  Score=85.41  Aligned_cols=47  Identities=11%  Similarity=0.188  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.|++|||||||+|++.++|++||+  ++..|+|+.|.|.++...
T Consensus        38 i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A           38 ILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTT
T ss_pred             EEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            46899999999999999999999999994  788999999999998654

>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=99.16  E-value=8.5e-12  Score=83.95  Aligned_cols=49  Identities=22%  Similarity=0.367  Sum_probs=39.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.||++||||||+|.+.++|++||  ++++.|+|+.|.|.++.+...
T Consensus        35 i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           35 FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH   85 (90)
T ss_dssp             EEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-----
T ss_pred             EEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCcc
Confidence            4678999999999999999999999999  478899999999999887543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.14  E-value=1.7e-11  Score=84.21  Aligned_cols=48  Identities=15%  Similarity=0.293  Sum_probs=43.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCC-cEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGG-STVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~g-r~i~v~~a~~~~   48 (234)
                      |++|+.|+++||||||+|.+.++|++||  ++++.|.| ++|.|.++.++.
T Consensus        44 i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~~   94 (100)
T 3ns6_A           44 FPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVE   94 (100)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHHH
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchhh
Confidence            6789999999999999999999999999  47889999 999999987643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.14  E-value=8.2e-11  Score=80.45  Aligned_cols=50  Identities=36%  Similarity=0.605  Sum_probs=45.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||+ +++.|.|+.|.|.++.++...
T Consensus        42 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~~~~~~   92 (99)
T 2dgs_A           42 MIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDSK   92 (99)
T ss_dssp             ECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECCCCCCC
T ss_pred             EEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECCCCccc
Confidence            46889999999999999999999999995 788999999999999876554

>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=99.13  E-value=1.4e-10  Score=79.20  Aligned_cols=50  Identities=24%  Similarity=0.349  Sum_probs=45.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|++|.|.++.++...
T Consensus        40 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccc
Confidence            57888899999999999999999999994  788999999999999887653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.13  E-value=8.9e-11  Score=79.73  Aligned_cols=50  Identities=24%  Similarity=0.384  Sum_probs=44.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|++|.|.++.++...
T Consensus        38 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   89 (96)
T 1x5t_A           38 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   89 (96)
T ss_dssp             ECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             EEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCC
Confidence            46888999999999999999999999995  688999999999999876543

>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=99.12  E-value=6e-11  Score=78.32  Aligned_cols=48  Identities=29%  Similarity=0.495  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++|+.  +++.|+|++|.|.++.++.
T Consensus        33 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             EEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            35788899999999999999999999994  7889999999999998754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.12  E-value=6.2e-11  Score=81.48  Aligned_cols=50  Identities=26%  Similarity=0.548  Sum_probs=45.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|+.|.|.++.++...
T Consensus        44 ~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            46788999999999999999999999994  788999999999999887654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.12  E-value=1.2e-10  Score=79.95  Aligned_cols=50  Identities=30%  Similarity=0.491  Sum_probs=45.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|++|.|.++.++...
T Consensus        44 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2cqb_A           44 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   95 (102)
T ss_dssp             CCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCC
Confidence            57889999999999999999999999994  788999999999999876543

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

Probab=99.12  E-value=8e-11  Score=81.14  Aligned_cols=50  Identities=24%  Similarity=0.494  Sum_probs=44.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|++.++|++|| ++++.|.|+.|.|.++.++...
T Consensus        46 i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           46 LVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECCCCCCC
T ss_pred             EeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEecCCCCC
Confidence            4678999999999999999999999999 4688999999999999876543

>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=99.11  E-value=1.8e-10  Score=80.34  Aligned_cols=51  Identities=16%  Similarity=0.349  Sum_probs=45.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--c------CceeCCcEEEEeeccCCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--D------THELGGSTVVVDRATPKEDDF   51 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~------~~~i~gr~i~v~~a~~~~~~~   51 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +      ++.|+|+.|.|.++.++....
T Consensus        47 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           47 VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             CCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCCC
T ss_pred             EEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccCC
Confidence            57899999999999999999999999994  6      789999999999998876543

>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=99.11  E-value=1.7e-10  Score=79.65  Aligned_cols=51  Identities=24%  Similarity=0.512  Sum_probs=45.2

Q ss_pred             CCCCCCC-CCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCCC
Q 026724            1 MPKDQGS-KAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDF   51 (234)
Q Consensus         1 l~rD~~t-g~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~~   51 (234)
                      |++|+.| ++++|||||+|.+.++|++|| ++++.|.|+.|.|.++.++....
T Consensus        46 i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~~~   98 (104)
T 1wi8_A           46 LPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKD   98 (104)
T ss_dssp             CCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCCCC
T ss_pred             EecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEccCCCCCC
Confidence            5788888 999999999999999999999 46789999999999998776543

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

Probab=99.10  E-value=6.8e-11  Score=76.55  Aligned_cols=44  Identities=36%  Similarity=0.594  Sum_probs=40.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      |++|+.|++++|||||+|.+.++|++|++ +++.|+|++|.|++|
T Consensus        31 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            57888899999999999999999999994 788999999999875

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=1.7e-10  Score=80.79  Aligned_cols=50  Identities=16%  Similarity=0.238  Sum_probs=45.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|+.|.|.++.++...
T Consensus        55 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           55 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             CCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             EEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCC
Confidence            56888999999999999999999999994  788999999999999876543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.10  E-value=1.5e-10  Score=80.70  Aligned_cols=50  Identities=30%  Similarity=0.541  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||+ .++.|+|+.|.|.++.++...
T Consensus        57 i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           57 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             ECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEECCCCCCC
T ss_pred             EEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEccCCCCC
Confidence            46889999999999999999999999996 458999999999999876543

>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=99.09  E-value=7.7e-11  Score=78.50  Aligned_cols=47  Identities=30%  Similarity=0.451  Sum_probs=41.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.|++++|||||+|.+.++|++|++  +++.|+|+.|.|.++.++
T Consensus        38 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           38 VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            45788899999999999999999999995  788999999999999764

>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=99.09  E-value=1.8e-10  Score=78.28  Aligned_cols=49  Identities=18%  Similarity=0.266  Sum_probs=44.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|++++|||||+|.+.++|++|++  ++..|+|+.|.|.++.++..
T Consensus        34 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             CCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            57889999999999999999999999994  78899999999999987653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=1.4e-10  Score=78.56  Aligned_cols=50  Identities=28%  Similarity=0.507  Sum_probs=44.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|++|+|.++.++...
T Consensus        37 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           37 LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             EECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             EeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            46788899999999999999999999995  788999999999999876543

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

Probab=99.08  E-value=1.7e-10  Score=81.19  Aligned_cols=51  Identities=35%  Similarity=0.580  Sum_probs=45.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDF   51 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~   51 (234)
                      |++|+.|++++|||||+|.+.++|++||. +++.|+|+.|.|.++.++....
T Consensus        59 i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~~~  110 (116)
T 1x4b_A           59 VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESG  110 (116)
T ss_dssp             EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCCCC
T ss_pred             EEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCCCccCC
Confidence            46788999999999999999999999995 6789999999999998876543

>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=99.07  E-value=2.1e-10  Score=79.20  Aligned_cols=50  Identities=30%  Similarity=0.588  Sum_probs=45.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|++|.|.++.++...
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           47 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             CCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             EEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            57888899999999999999999999995  688999999999999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=1.6e-10  Score=79.58  Aligned_cols=50  Identities=18%  Similarity=0.378  Sum_probs=44.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|+.|.|.++.++...
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           47 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             EeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            46788899999999999999999999995  788999999999999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.06  E-value=1.5e-10  Score=79.78  Aligned_cols=50  Identities=28%  Similarity=0.478  Sum_probs=44.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|+|+.|.|.++.+....
T Consensus        45 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dnm_A           45 IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD   96 (103)
T ss_dssp             CCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSC
T ss_pred             EEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCC
Confidence            57889999999999999999999999995  788999999999999876543

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

Probab=99.06  E-value=1e-10  Score=80.28  Aligned_cols=40  Identities=25%  Similarity=0.378  Sum_probs=36.4

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++|||||+|.+.++|++|++  ++..|+|+.|.|.++.++..
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            79999999999999999995  67899999999999987654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.06  E-value=3.7e-10  Score=79.32  Aligned_cols=51  Identities=27%  Similarity=0.381  Sum_probs=45.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDF   51 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~   51 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|+.|.|.++.++....
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           47 VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCCS
T ss_pred             EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCCC
Confidence            46788899999999999999999999994  7889999999999998775543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.05  E-value=1.7e-10  Score=79.23  Aligned_cols=50  Identities=30%  Similarity=0.610  Sum_probs=44.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|++|.|.++.++...
T Consensus        44 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             EEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            46888999999999999999999999994  788999999999999876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.05  E-value=8.4e-11  Score=80.68  Aligned_cols=49  Identities=16%  Similarity=0.403  Sum_probs=43.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +++|+.|+++||||||+|.+.++|++|| ++++.|.|+.|.|.++.++..
T Consensus        48 ~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           48 AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCSCCCC
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcCCCCC
Confidence            4678889999999999999999999999 477899999999999987654

>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=99.05  E-value=1.2e-10  Score=81.88  Aligned_cols=47  Identities=17%  Similarity=0.258  Sum_probs=42.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+ |+++||||||+|++.++|++||+ +++.|+|+.|.|.++.++.
T Consensus        48 i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           48 VLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLED   95 (114)
T ss_dssp             ECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECHHH
T ss_pred             EEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEECCHHH
Confidence            46888 89999999999999999999995 6789999999999987653

>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=99.05  E-value=2.7e-10  Score=79.34  Aligned_cols=48  Identities=17%  Similarity=0.248  Sum_probs=44.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|+|+.|.|.++.++.
T Consensus        58 i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           58 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             CCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            57889999999999999999999999994  7889999999999998764

>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=99.05  E-value=1.8e-10  Score=80.97  Aligned_cols=50  Identities=16%  Similarity=0.322  Sum_probs=44.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||+  +++.|.|+.|+|.++.++...
T Consensus        57 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~  108 (115)
T 2cpz_A           57 VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  108 (115)
T ss_dssp             EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             EEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcC
Confidence            46788899999999999999999999994  788999999999999876543

>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=99.04  E-value=8.4e-11  Score=80.99  Aligned_cols=47  Identities=13%  Similarity=0.099  Sum_probs=41.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+ |+++||||||+|++.++|++||+ +++.|+++.|.|.++.+..
T Consensus        46 i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           46 IEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             EEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCC
T ss_pred             EEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCCCC
Confidence            46787 89999999999999999999994 6789999999999887654

>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=99.04  E-value=1.1e-10  Score=75.54  Aligned_cols=44  Identities=32%  Similarity=0.561  Sum_probs=40.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      |++|+.|++++|||||+|.+.++|++|++ +++.|.|+.|.|++|
T Consensus        31 i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             EEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            57889999999999999999999999995 678999999999875

>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=99.04  E-value=1.6e-10  Score=77.05  Aligned_cols=44  Identities=34%  Similarity=0.575  Sum_probs=40.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      |++|+.|++++|||||+|.+.++|++||+ +++.|+|+.|.|++|
T Consensus        43 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           43 IKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             EEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             EeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            46788999999999999999999999995 577999999999875

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

Probab=99.04  E-value=1.5e-10  Score=79.88  Aligned_cols=51  Identities=24%  Similarity=0.408  Sum_probs=43.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCce-eCCcEEEEeeccCCCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHE-LGGSTVVVDRATPKEDDFR   52 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~-i~gr~i~v~~a~~~~~~~~   52 (234)
                      |++|+ |++++|||||+|.+.++|++||+  +++. |+|++|.|.++.++.....
T Consensus        42 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~~   95 (104)
T 2dhg_A           42 VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVK   95 (104)
T ss_dssp             EEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSCCC
T ss_pred             EEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcCCC
Confidence            45788 89999999999999999999995  6777 9999999999987665443

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=2.9e-10  Score=76.80  Aligned_cols=45  Identities=27%  Similarity=0.458  Sum_probs=41.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|++|+|.+|.
T Consensus        48 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           48 IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             ECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             EEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            46888999999999999999999999994  7889999999999873

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=1.2e-10  Score=80.53  Aligned_cols=50  Identities=26%  Similarity=0.547  Sum_probs=44.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|++.++|++||. +++.|+|+.|.|.++.++...
T Consensus        48 i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a~~~~~~   98 (105)
T 2dh8_A           48 IMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQ   98 (105)
T ss_dssp             EEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCSCCSSCC
T ss_pred             EeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEccCCCCC
Confidence            46788999999999999999999999996 788999999999999877654

>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=99.03  E-value=2.2e-10  Score=75.88  Aligned_cols=45  Identities=31%  Similarity=0.554  Sum_probs=41.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.|++++|||||+|.+.++|++|+  ++++.|+|++|+|.++.
T Consensus        39 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            5678899999999999999999999999  47889999999999873

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=1.9e-10  Score=80.10  Aligned_cols=45  Identities=22%  Similarity=0.226  Sum_probs=40.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+. |++||||||+|++.++|++||+ +++.|+||.|.|..+.+
T Consensus        47 i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           47 LLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             ECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             EEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            467876 9999999999999999999994 78899999999988764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=2.3e-10  Score=76.91  Aligned_cols=47  Identities=17%  Similarity=0.362  Sum_probs=41.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++| .+++++|||||+|.+.++|++||. ++..|.|+.|.|.++.++.
T Consensus        41 i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           41 IVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             EEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEESSCC
T ss_pred             EEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECCcCC
Confidence            3567 789999999999999999999995 6779999999999998764

>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=99.03  E-value=1.9e-10  Score=78.83  Aligned_cols=48  Identities=23%  Similarity=0.533  Sum_probs=42.7

Q ss_pred             CCCCC-CCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQ-GSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~-~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+ .|++++|||||+|.+.++|++|| ++++.|.|+.|.|.++.++.
T Consensus        50 i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           50 LPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             CSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEECCCSC
T ss_pred             EEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEeccCCC
Confidence            56787 69999999999999999999999 36889999999999987653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.03  E-value=7.9e-10  Score=77.76  Aligned_cols=49  Identities=24%  Similarity=0.331  Sum_probs=42.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|++++|||||+|.+.++|++||+. ...|.|+.|.|+++.++..
T Consensus        49 i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~   98 (116)
T 2cqd_A           49 VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAK   98 (116)
T ss_dssp             ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTTCC
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEcccCCC
Confidence            578899999999999999999999999953 3389999999999976543

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

Probab=99.03  E-value=1.7e-10  Score=79.89  Aligned_cols=48  Identities=15%  Similarity=0.286  Sum_probs=43.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|+.|.|.++.++.
T Consensus        55 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           55 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             EEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             EEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            45788999999999999999999999994  7889999999999998654

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

Probab=99.03  E-value=1.2e-10  Score=86.55  Aligned_cols=47  Identities=26%  Similarity=0.356  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.||++||||||+|.+.++|++||.  +++.|+|+.|.|.++.++
T Consensus        89 i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           89 FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            46899999999999999999999999994  788999999999998754

>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=99.03  E-value=4.6e-10  Score=77.60  Aligned_cols=50  Identities=18%  Similarity=0.282  Sum_probs=43.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCcee---CCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHEL---GGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i---~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||.  ++..+   .+++|.|.++.++...
T Consensus        45 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           45 VLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             CCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            57899999999999999999999999994  67676   8899999999876543

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

Probab=99.02  E-value=3.2e-10  Score=77.58  Aligned_cols=48  Identities=6%  Similarity=0.280  Sum_probs=42.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+ +++++|||||+|.+.++|++||+  +++.|.|++|.|.++.++..
T Consensus        49 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           49 LVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             EEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             EEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            35677 89999999999999999999994  78899999999999987653

>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=99.02  E-value=8.8e-10  Score=76.57  Aligned_cols=47  Identities=23%  Similarity=0.340  Sum_probs=42.3

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHHh--c--CceeCCcEEEEeeccCCCC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLMV--D--THELGGSTVVVDRATPKED   49 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al~--~--~~~i~gr~i~v~~a~~~~~   49 (234)
                      +|+.|+++||||||+|.+.++|++||.  +  +..|+|+.|.|.++.++..
T Consensus        44 ~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           44 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             SSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             cCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            788999999999999999999999995  3  3789999999999987654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.02  E-value=2.7e-10  Score=77.08  Aligned_cols=46  Identities=26%  Similarity=0.442  Sum_probs=41.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|+|++|.|.++.+
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             EEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            45788999999999999999999999995  78899999999999864

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.02  E-value=5.7e-10  Score=77.22  Aligned_cols=50  Identities=28%  Similarity=0.554  Sum_probs=44.3

Q ss_pred             CCCC-CCCCCccceEEEEEcCHHHHHHHHh---cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKD-QGSKAHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD-~~tg~srG~aFV~F~~~e~A~~Al~---~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++| +.+++++|||||+|.+.++|++||.   +++.|.|+.|.|.++.++...
T Consensus        47 i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~  100 (107)
T 2cph_A           47 LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV  100 (107)
T ss_dssp             CCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCC
T ss_pred             EecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCC
Confidence            5677 7899999999999999999999994   688999999999999876543

>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=99.01  E-value=4.2e-10  Score=77.67  Aligned_cols=47  Identities=21%  Similarity=0.371  Sum_probs=41.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++| .|++++|||||+|++.++|++||. +++.|+++.|.|.++..+.
T Consensus        48 i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           48 LPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             CCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTT
T ss_pred             EEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEECCHHH
Confidence            4677 789999999999999999999995 6789999999999887654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.01  E-value=1.9e-10  Score=78.67  Aligned_cols=45  Identities=22%  Similarity=0.342  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|.|+.|+|++|.
T Consensus        53 i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           53 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             EEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             EEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            45788999999999999999999999994  7889999999999873

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.01  E-value=8.1e-10  Score=75.69  Aligned_cols=48  Identities=21%  Similarity=0.506  Sum_probs=42.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++| .+++++|||||+|.+.++|++||.  +++.|.|+.|.|.++.++..
T Consensus        44 ~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (101)
T 2fc9_A           44 VPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGS   93 (101)
T ss_dssp             CCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCC
T ss_pred             EEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCC
Confidence            4556 689999999999999999999995  78899999999999987654

>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=99.01  E-value=2.7e-10  Score=77.68  Aligned_cols=46  Identities=15%  Similarity=0.231  Sum_probs=41.5

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++|+.|++++|||||+|.+.++|++||+  +++.|.|+.|+|+++..+
T Consensus        48 ~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           48 LKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             EEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             EEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            5678899999999999999999999994  678999999999998754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.00  E-value=3.3e-10  Score=81.57  Aligned_cols=48  Identities=23%  Similarity=0.429  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCc----eeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTH----ELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~----~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+++||||||+|.+. +|++||+  ++.    .|+|+.|.|+++.++..
T Consensus        57 i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           57 VIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             EEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            678999999999999999999 9999994  677    99999999999987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.00  E-value=5.6e-10  Score=81.10  Aligned_cols=50  Identities=20%  Similarity=0.371  Sum_probs=44.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|.|+.|.|.++.++...
T Consensus        74 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           74 IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            45788899999999999999999999995  688999999999999876554

>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=99.00  E-value=3.1e-10  Score=75.87  Aligned_cols=47  Identities=21%  Similarity=0.333  Sum_probs=42.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.|++++|||||+|.+.++|++|+ ++++.|.|+.|.|.++.+.
T Consensus        38 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           38 ILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             EEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            4578889999999999999999999999 4688999999999998754

>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=99.00  E-value=1.9e-10  Score=80.05  Aligned_cols=48  Identities=25%  Similarity=0.487  Sum_probs=43.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++||+  ++..|.|++|.|.++.++.
T Consensus        58 i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           58 LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             EEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            45788899999999999999999999994  7889999999999998764

>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=99.00  E-value=7.8e-10  Score=82.06  Aligned_cols=49  Identities=29%  Similarity=0.451  Sum_probs=44.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+++||||||+|.+.++|++||.  +++.|.|++|.|.++.++..
T Consensus       102 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A          102 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             CCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             EeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            57899999999999999999999999994  78899999999999987643

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=98.99  E-value=3.1e-10  Score=81.54  Aligned_cols=48  Identities=29%  Similarity=0.452  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|+|++|.|.++.++.
T Consensus        78 i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           78 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             EECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            46788999999999999999999999995  7889999999999998754

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=98.99  E-value=7.1e-10  Score=78.13  Aligned_cols=48  Identities=27%  Similarity=0.450  Sum_probs=42.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+ |++++|||||+|.+.++|++||+  ++..|.|+.|.|.++.++..
T Consensus        39 i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           39 LIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             EECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             EEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            35677 89999999999999999999995  78899999999999987654

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=98.98  E-value=3.2e-10  Score=76.81  Aligned_cols=46  Identities=15%  Similarity=0.275  Sum_probs=40.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.+++++|||||+|.+.++|++||+  +++.|.|++|+|.++.+
T Consensus        47 ~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             EEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             EEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            35678899999999999999999999994  78899999999998753

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=98.97  E-value=6.3e-10  Score=79.41  Aligned_cols=50  Identities=14%  Similarity=0.266  Sum_probs=45.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|.|+.|.|.++.++...
T Consensus        54 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           54 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP  105 (126)
T ss_dssp             CCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSC
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCC
Confidence            57888999999999999999999999994  788999999999999876543

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=2e-09  Score=71.63  Aligned_cols=73  Identities=19%  Similarity=0.245  Sum_probs=60.6

Q ss_pred             CCCCCEEEEeCCCCC-----CCH----HHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeE
Q 026724           98 QRIGKKIFVGRLPQE-----ATA----EDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQ  167 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~-----~~~----~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~  167 (234)
                      -++..+|+|.-++..     +-.    .+|.+.|++||+|..++++.+     -+||+|.+.++|.+|| +++..++|+.
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-----~~fVtF~d~~sAl~AI~ldG~~v~Gr~   86 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----QMLVTFADSHSALSVLDVDGMKVKGRA   86 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----EEEEECSCSHHHHHHHHGGGSEETTEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-----cEEEEEcChHHHHHHHhcCCeeeCCeE
Confidence            446789999988743     322    568999999999999999854     2999999999999999 5888999999


Q ss_pred             eEEEeCCC
Q 026724          168 VAIDSATP  175 (234)
Q Consensus       168 i~v~~a~~  175 (234)
                      |+|++..+
T Consensus        87 L~V~~k~~   94 (95)
T 1ufw_A           87 VKISGPSS   94 (95)
T ss_dssp             EEEECCCC
T ss_pred             EEEeccCC
Confidence            99987653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.96  E-value=3.6e-10  Score=77.17  Aligned_cols=48  Identities=21%  Similarity=0.299  Sum_probs=42.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcE----EEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGST----VVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~----i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|+.    |+|.++.+..
T Consensus        42 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~   95 (99)
T 2div_A           42 IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSG   95 (99)
T ss_dssp             EEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCS
T ss_pred             EeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCC
Confidence            46788999999999999999999999995  688999999    9999987653

>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=98.96  E-value=3e-10  Score=79.70  Aligned_cols=48  Identities=21%  Similarity=0.453  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++|| ++++.|.|+.|.|.++.++.
T Consensus        57 i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           57 IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK  105 (114)
T ss_dssp             ECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHHH
T ss_pred             EEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCCCc
Confidence            4689999999999999999999999999 47889999999999987653

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

Probab=98.95  E-value=4e-10  Score=77.71  Aligned_cols=45  Identities=18%  Similarity=0.276  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+. +++||||||+|++.++|++||. +++.|+|+.|.|.++..
T Consensus        43 i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           43 MRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             EECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHHH
T ss_pred             EEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEchH
Confidence            467887 9999999999999999999995 68899999999998764

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.95  E-value=1e-09  Score=76.59  Aligned_cols=47  Identities=11%  Similarity=0.180  Sum_probs=40.5

Q ss_pred             CCCCCCC---CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            2 PKDQGSK---AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         2 ~rD~~tg---~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++|+.|+   +++|||||+|++.++|++||+  +++.|+|++|.|.++.++.
T Consensus        51 ~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           51 NNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             ECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             ecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            4566644   566999999999999999994  7889999999999998775

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.94  E-value=4.2e-10  Score=76.67  Aligned_cols=49  Identities=14%  Similarity=0.332  Sum_probs=42.0

Q ss_pred             CCCCC---CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            2 PKDQG---SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         2 ~rD~~---tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ++|+.   |++++|||||+|.+.++|++||.  +++.|.|++|.|.++.++...
T Consensus        38 ~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (98)
T 2cpf_A           38 SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKP   91 (98)
T ss_dssp             EEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCC
T ss_pred             EecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCC
Confidence            34555   77999999999999999999995  788999999999999876543

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=3.4e-10  Score=78.00  Aligned_cols=49  Identities=20%  Similarity=0.435  Sum_probs=43.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|++++|||||+|.+.++|++|++  +++.|.|+.|.|.++.++..
T Consensus        40 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   90 (104)
T 1p1t_A           40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN   90 (104)
T ss_dssp             EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTH
T ss_pred             EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCccc
Confidence            35678899999999999999999999994  78899999999999987643

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

Probab=98.94  E-value=3e-10  Score=76.14  Aligned_cols=48  Identities=27%  Similarity=0.535  Sum_probs=39.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|++++|||||+|.+.+ |++|++  +++.|+|++|.|++|.++..
T Consensus        33 i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~   82 (90)
T 2ki2_A           33 LIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKS   82 (90)
T ss_dssp             ECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC-----
T ss_pred             EEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            4688999999999999999999 999995  68899999999999987644

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=98.93  E-value=2.5e-10  Score=81.51  Aligned_cols=46  Identities=22%  Similarity=0.374  Sum_probs=41.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+. |++||||||+|++.++|++||+ ++..|+||.|.|..+.++
T Consensus        75 i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a~~~  121 (126)
T 2hgm_A           75 LPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE  121 (126)
T ss_dssp             CCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEECHH
T ss_pred             EEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCHH
Confidence            578888 9999999999999999999995 578999999999888643

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=98.93  E-value=8.8e-10  Score=81.68  Aligned_cols=50  Identities=22%  Similarity=0.277  Sum_probs=44.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||+  +++.|+|+.|.|.++.++...
T Consensus        71 i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  122 (156)
T 1h2v_Z           71 MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEG  122 (156)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCTT
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCc
Confidence            46789999999999999999999999995  788999999999999876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.93  E-value=1.1e-09  Score=77.87  Aligned_cols=48  Identities=25%  Similarity=0.320  Sum_probs=42.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|++++|||||+|.+.++|++||. +++.|+|+.|.|.++.+..
T Consensus        68 i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~  116 (124)
T 2jwn_A           68 ILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNM  116 (124)
T ss_dssp             EEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSCCC
T ss_pred             EEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCCCC
Confidence            35788899999999999999999999993 6889999999999987543

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

Probab=98.93  E-value=8.2e-10  Score=79.94  Aligned_cols=49  Identities=29%  Similarity=0.451  Sum_probs=44.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+++||||||+|.+.++|++||.  +++.|.|++|.|.++.++..
T Consensus        79 i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           79 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            57888999999999999999999999994  78899999999999986543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.93  E-value=5.2e-10  Score=79.08  Aligned_cols=46  Identities=17%  Similarity=0.263  Sum_probs=40.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+. |++||||||+|++.++|++||+ +++.|+|+.|.|.++..+
T Consensus        52 i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           52 FIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             EEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEEEECHH
T ss_pred             EEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCHH
Confidence            356777 9999999999999999999995 788999999999998654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=98.93  E-value=4e-10  Score=81.56  Aligned_cols=46  Identities=17%  Similarity=0.272  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+. |++||||||+|++.++|++||+ +++.|+|+.|.|.++.++
T Consensus        79 i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           79 FIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             EEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEEECCHH
T ss_pred             EEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEEECChH
Confidence            457887 9999999999999999999995 778999999999988654

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

Probab=98.92  E-value=3.2e-10  Score=73.64  Aligned_cols=44  Identities=32%  Similarity=0.549  Sum_probs=39.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a   44 (234)
                      |++|+.|++++|||||+|.+.++|++|++. .+.|+|++|.|++|
T Consensus        32 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a   76 (77)
T 1uaw_A           32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             EECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             EecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            467889999999999999999999999952 37999999999987

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=98.92  E-value=3.1e-10  Score=79.72  Aligned_cols=65  Identities=12%  Similarity=0.230  Sum_probs=54.8

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcCCCCcc
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (234)
                      ++.++|||||+|.+.++|++|+.  ++..|+|+.|.|.++.++...                                  
T Consensus        43 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~----------------------------------   88 (115)
T 3lqv_A           43 TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF----------------------------------   88 (115)
T ss_dssp             STTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT----------------------------------
T ss_pred             CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh----------------------------------
Confidence            35679999999999999999995  788999999999998754321                                  


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCc
Q 026724           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR  127 (234)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~  127 (234)
                                            .+++...++++|+++|++||.
T Consensus        89 ----------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           89 ----------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             ----------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             ----------------------hhhhHhHhHHHHHHHHHHhCC
Confidence                                  356777899999999999985

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=98.92  E-value=9.1e-10  Score=73.33  Aligned_cols=48  Identities=17%  Similarity=0.377  Sum_probs=41.9

Q ss_pred             CCCCCCCCC-ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKA-HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~-srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|+. ++|||||+|.+.++|++|++  ++..|+|+.|.|.++.+..
T Consensus        36 i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           36 MPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             CCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             EEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            456777766 99999999999999999995  7899999999999997643

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=2.1e-09  Score=72.98  Aligned_cols=45  Identities=9%  Similarity=0.132  Sum_probs=39.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|   ||||||+|.+.++|++||+  ++..|+|++|+|.++.++.
T Consensus        45 i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           45 LSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             ECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             EEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            4567776   8999999999999999994  7889999999999997654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=1.2e-09  Score=75.15  Aligned_cols=47  Identities=19%  Similarity=0.365  Sum_probs=41.7

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ++|  +++++|||||+|.+.++|++||+  +++.|.|++|.|.++.++...
T Consensus        48 ~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2d9p_A           48 MME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEER   96 (103)
T ss_dssp             EEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCC
T ss_pred             EcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccC
Confidence            455  89999999999999999999995  788999999999999877654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.91  E-value=1.1e-09  Score=75.68  Aligned_cols=46  Identities=15%  Similarity=0.152  Sum_probs=40.2

Q ss_pred             CCCCCCC-CCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            1 MPKDQGS-KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~t-g~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.+ ++++|||||+|++.++|++|+  +++..|+||.|.|.++..
T Consensus        45 i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           45 IFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             EEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             EecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            3567654 799999999999999999999  478999999999999864

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=98.90  E-value=5.1e-10  Score=77.67  Aligned_cols=46  Identities=17%  Similarity=0.218  Sum_probs=41.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+. |++||||||+|.+.++|++||. +++.|+|+.|.|.++.++
T Consensus        46 i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           46 FLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             CCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCEECCHH
T ss_pred             EEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEEECCHH
Confidence            577888 9999999999999999999995 678999999999988754

>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=98.90  E-value=1.1e-09  Score=75.48  Aligned_cols=49  Identities=16%  Similarity=0.294  Sum_probs=42.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCC---cEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG---STVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~g---r~i~v~~a~~~~~~   50 (234)
                      |++|+ +++++|||||+|.+.++|++||+  ++..|.+   ++|.|.++.++...
T Consensus        47 i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           47 VLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES  100 (105)
T ss_dssp             EEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCC
T ss_pred             EEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCccc
Confidence            35676 79999999999999999999994  7778887   99999999876543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.90  E-value=2.5e-09  Score=76.12  Aligned_cols=48  Identities=17%  Similarity=0.185  Sum_probs=42.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+ |++++|||||+|.+.++|++||.  ++..|.|+.|.|.+|.+...
T Consensus        67 i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  116 (124)
T 2kt5_A           67 VDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID  116 (124)
T ss_dssp             EECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTC
T ss_pred             EEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            35677 89999999999999999999995  78899999999999987543

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

Probab=98.90  E-value=7e-10  Score=78.23  Aligned_cols=45  Identities=18%  Similarity=0.348  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|+|+.|+|+++.
T Consensus        72 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           72 VFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             ECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             EEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            46788999999999999999999999995  6889999999999863

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.90  E-value=3.2e-10  Score=80.86  Aligned_cols=46  Identities=17%  Similarity=0.252  Sum_probs=41.3

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      +.|..|++++|||||+|++.++|++||+ +++.|+|+.|.|.++.++
T Consensus        58 ~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~~  104 (124)
T 1wel_A           58 IAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKK  104 (124)
T ss_dssp             EEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECHH
T ss_pred             EEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCHH
Confidence            4567799999999999999999999995 788999999999998754

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=98.89  E-value=1.3e-09  Score=75.47  Aligned_cols=44  Identities=18%  Similarity=0.203  Sum_probs=39.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      |++|+ |++++|||||+|.+.++|++||+  ++..|.|+.|.|.++.
T Consensus        61 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           61 VHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             EEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            35677 89999999999999999999995  7889999999999875

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

Probab=98.41  E-value=1.8e-10  Score=81.12  Aligned_cols=50  Identities=22%  Similarity=0.321  Sum_probs=44.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||.  ++..|.|++|.|.++.++...
T Consensus        47 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           47 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            46788899999999999999999999995  788999999999999877554

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.88  E-value=4.3e-09  Score=73.62  Aligned_cols=47  Identities=19%  Similarity=0.223  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+ +++++|||||+|.+.++|++||+  +++.|+|+.|.|+++....
T Consensus        47 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   95 (114)
T 2do0_A           47 ILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL   95 (114)
T ss_dssp             EEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCC
T ss_pred             EEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCC
Confidence            35666 59999999999999999999995  7889999999999987543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.88  E-value=4.6e-10  Score=79.86  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=40.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      |++| .||++||||||+|++.++|++||+ +++.|.+|.|.|..+.++
T Consensus        59 i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~~a~~~  105 (123)
T 2dha_A           59 FVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA  105 (123)
T ss_dssp             EEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCEEECHH
T ss_pred             EEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEEECCHH
Confidence            3567 489999999999999999999995 678999999999887644

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=98.87  E-value=6.1e-10  Score=87.86  Aligned_cols=47  Identities=21%  Similarity=0.339  Sum_probs=42.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.|+++||||||+|++.++|++||+  +++.|+|+.|.|.++.+.
T Consensus       102 i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C          102 FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             EEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHH
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCC
Confidence            56899999999999999999999999995  678999999999998754

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.87  E-value=1.8e-09  Score=74.49  Aligned_cols=43  Identities=12%  Similarity=0.296  Sum_probs=37.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a   44 (234)
                      |++|+. +++||||||+|.+.++|++|+  +++..|+||+|.|.++
T Consensus        59 i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           59 VCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             ECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             EEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            356654 799999999999999999999  4789999999999875

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.86  E-value=2.9e-09  Score=70.37  Aligned_cols=38  Identities=11%  Similarity=0.338  Sum_probs=34.6

Q ss_pred             CCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeecc
Q 026724            8 KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRAT   45 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~   45 (234)
                      ..|||||||+|.++++|++|+  +|+..|.|++|+|++|.
T Consensus        40 ~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           40 YLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            348999999999999999999  47889999999999984

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=4.8e-09  Score=72.03  Aligned_cols=47  Identities=15%  Similarity=0.239  Sum_probs=39.9

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ++|+.  .+||||||+|.+.++|++||.  +++.|.|++|.|.++.++...
T Consensus        48 ~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           48 ITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             ECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             EecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence            45544  479999999999999999994  788999999999999876543

>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=98.86  E-value=1.5e-09  Score=73.44  Aligned_cols=45  Identities=22%  Similarity=0.392  Sum_probs=39.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+. ++++|||||+|.+.++|++||+  +++.|.|++|.|.++..
T Consensus        48 i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           48 ICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             EEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             EEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            356765 9999999999999999999995  78899999999998753

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=4.1e-10  Score=74.62  Aligned_cols=45  Identities=13%  Similarity=0.288  Sum_probs=39.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.|++++|||||+|.+.++|++|++  +++.|.|+.|+|.++.
T Consensus        37 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           37 AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            46788999999999999999999999995  6789999998877654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.85  E-value=5.4e-10  Score=76.74  Aligned_cols=48  Identities=19%  Similarity=0.421  Sum_probs=42.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+ |+++||||||+|++.++|++||.+++.|+|+.|.|.++.++..
T Consensus        41 i~~~~-~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           41 IITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRKQN   88 (102)
T ss_dssp             EEECT-TSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEECC-
T ss_pred             EEECC-CCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCcCcc
Confidence            45777 8999999999999999999999988899999999999987654

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=98.85  E-value=6.4e-10  Score=80.78  Aligned_cols=48  Identities=10%  Similarity=0.081  Sum_probs=42.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+. +++||||||+|++.++|++||+ +++.|.++.|.|.++.++..
T Consensus        77 i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           77 IEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSCC
T ss_pred             EEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCCC
Confidence            578887 9999999999999999999994 67899999999998876543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.84  E-value=3.1e-09  Score=73.37  Aligned_cols=44  Identities=20%  Similarity=0.234  Sum_probs=39.5

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCc-EEEEeeccCCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGS-TVVVDRATPKE   48 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr-~i~v~~a~~~~   48 (234)
                      +.||++||||||+|.+.++|++||.  +++.|+|+ +|.|.++....
T Consensus        55 ~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           55 EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCCC
T ss_pred             CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchHh
Confidence            4689999999999999999999995  78899999 99999987543

>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=98.83  E-value=5e-09  Score=72.35  Aligned_cols=46  Identities=20%  Similarity=0.338  Sum_probs=40.1

Q ss_pred             CCCCCCC--CCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            1 MPKDQGS--KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~t--g~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.+  ++++|||||+|++.++|++|+  +++..++||+|.|.++..
T Consensus        47 i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           47 IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             CCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             EeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCH
Confidence            5677765  479999999999999999999  489999999999998754

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=98.83  E-value=2.3e-09  Score=80.23  Aligned_cols=49  Identities=16%  Similarity=0.239  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|++++|||||+|.+.++|++||.  ++..|.|++|.|.++.++..
T Consensus       104 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A          104 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             EEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            45788999999999999999999999994  78899999999999987654

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

Probab=98.82  E-value=2.6e-09  Score=74.89  Aligned_cols=47  Identities=21%  Similarity=0.290  Sum_probs=41.3

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      +..|++++|||||+|.+.++|++||.  +++.|.|++|.|.++.++...
T Consensus        60 ~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  108 (115)
T 2cpx_A           60 RMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  108 (115)
T ss_dssp             EEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             EcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCC
Confidence            34489999999999999999999994  788999999999999876543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.82  E-value=2.5e-09  Score=76.47  Aligned_cols=44  Identities=18%  Similarity=0.345  Sum_probs=39.5

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .|+++||||||+|.+.++|++||.  ++..|.|++|.|.++..+..
T Consensus        67 ~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           67 LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS  112 (127)
T ss_dssp             CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCCH
T ss_pred             cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcch
Confidence            478999999999999999999994  78899999999999987643

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.81  E-value=7.5e-09  Score=71.05  Aligned_cols=47  Identities=19%  Similarity=0.349  Sum_probs=40.1

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ++|+.  .++|||||+|.+.++|++||.  +++.|+|+.|.|.++.++...
T Consensus        48 ~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           48 IFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT   96 (103)
T ss_dssp             ECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCC
T ss_pred             EecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCC
Confidence            45544  499999999999999999994  788999999999999876543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.81  E-value=5.8e-09  Score=70.64  Aligned_cols=45  Identities=22%  Similarity=0.347  Sum_probs=39.8

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ..+++++|||||+|.+.++|++||.  +++.|.|+.|.|.++.++..
T Consensus        47 ~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           47 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            3578999999999999999999995  67899999999999987643

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

Probab=98.78  E-value=3.3e-09  Score=71.21  Aligned_cols=44  Identities=18%  Similarity=0.295  Sum_probs=39.5

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .+++++|||||+|.+.++|++||+  +++.|+|+.|.|.++.+...
T Consensus        43 ~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   88 (92)
T 2dgv_A           43 ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASG   88 (92)
T ss_dssp             SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSS
T ss_pred             cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            478999999999999999999995  78899999999999987643

>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=98.77  E-value=4.7e-09  Score=73.47  Aligned_cols=46  Identities=20%  Similarity=0.397  Sum_probs=39.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCcee--------CCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHEL--------GGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i--------~gr~i~v~~a~~~   47 (234)
                      |++|+ |+++||||||+|.+.++|++||.  ++..|        .+++|.|.++.++
T Consensus        57 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           57 ILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             EEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             EEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            45677 89999999999999999999994  67777        6888999998754

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

Probab=98.77  E-value=9.6e-09  Score=71.97  Aligned_cols=46  Identities=22%  Similarity=0.313  Sum_probs=39.5

Q ss_pred             CCCCCCC---CCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccC
Q 026724            1 MPKDQGS---KAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~t---g~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~   46 (234)
                      +++|+.|   |++||||||+|++.++|++||+..+.++|+.|.+..+..
T Consensus        39 ~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~~~~~   87 (114)
T 2dnl_A           39 WPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPT   87 (114)
T ss_dssp             CTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEECCSS
T ss_pred             EeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEeccCCC
Confidence            4567777   799999999999999999999888889999998876543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.77  E-value=2.7e-09  Score=75.43  Aligned_cols=45  Identities=16%  Similarity=0.019  Sum_probs=37.3

Q ss_pred             CCCCCCCCCccceEEEEEcC----HHH----HHHHHh----cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFAS----ADS----VENLMV----DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~----~e~----A~~Al~----~~~~i~gr~i~v~~a~   45 (234)
                      |+.|+.||+|+|||||+|.+    +++    |.+|+.    ++..|+|++|+|.+..
T Consensus        38 li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           38 AFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             EEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECC
T ss_pred             EEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECc
Confidence            46899999999999999996    433    788875    6889999999998754

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.76  E-value=1.5e-08  Score=70.33  Aligned_cols=45  Identities=13%  Similarity=0.265  Sum_probs=39.2

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      .+++++|||||+|++.++|++||+  +++.|+|+.|.|.++.++...
T Consensus        56 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  102 (109)
T 1x4a_A           56 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT  102 (109)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCC
T ss_pred             ECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCCC
Confidence            356799999999999999999994  788999999999999876543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=1.2e-08  Score=69.63  Aligned_cols=42  Identities=12%  Similarity=0.188  Sum_probs=37.6

Q ss_pred             CCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCC
Q 026724            8 KAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +++||||||+|++.++|++||..++.+.+++|.|.|+.++..
T Consensus        51 ~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           51 SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECSSCCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEccCCCC
Confidence            479999999999999999999888888999999999876643

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.73  E-value=2.6e-08  Score=77.96  Aligned_cols=74  Identities=11%  Similarity=0.154  Sum_probs=60.0

Q ss_pred             CCEEEEeCCC-----CCCCHHHHHHHHhhcCceeEEEee------cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCe
Q 026724          101 GKKIFVGRLP-----QEATAEDLRRYFSRFGRILDVYVP------KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQ  166 (234)
Q Consensus       101 ~~~l~v~nl~-----~~~~~~~l~~~f~~~G~v~~~~~~------~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~  166 (234)
                      ...+.+.|+-     ..-.+++|.+.|++||.|.++.|+      +.++ ++|++||+|.+.++|.+|+  +++..++||
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            4455555552     234678999999999999999987      2334 7899999999999999998  588899999


Q ss_pred             EeEEEeCC
Q 026724          167 QVAIDSAT  174 (234)
Q Consensus       167 ~i~v~~a~  174 (234)
                      .|.|.+..
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999875

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.73  E-value=5.2e-09  Score=68.60  Aligned_cols=37  Identities=22%  Similarity=0.288  Sum_probs=33.4

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCc-EEEE
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGS-TVVV   41 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr-~i~v   41 (234)
                      +.||++||||||+|.+.++|++|+.  ++..|+|+ +|+|
T Consensus        41 ~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           41 EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4689999999999999999999995  78899999 8876

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.72  E-value=1.6e-08  Score=70.46  Aligned_cols=40  Identities=23%  Similarity=0.434  Sum_probs=35.7

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      .+++|||||+|++.++|++||+  ++..|+|+.|.|.++...
T Consensus        64 ~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            4699999999999999999994  788999999999998654

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=98.71  E-value=6.7e-09  Score=75.74  Aligned_cols=45  Identities=18%  Similarity=0.217  Sum_probs=40.4

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ..|++++|||||+|.+.++|++||.  ++..|.|+.|.|.++.+...
T Consensus        86 ~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~  132 (143)
T 3egn_A           86 MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP  132 (143)
T ss_dssp             EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCSCC
T ss_pred             ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            4689999999999999999999994  78899999999999976543

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

Probab=98.70  E-value=1.1e-08  Score=71.02  Aligned_cols=44  Identities=20%  Similarity=0.437  Sum_probs=38.4

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++|+  +.+||||||+|.+.++|++|++  +++.|+|+.|.|.++.++
T Consensus        62 ~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           62 IFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             CCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             EECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            4554  4599999999999999999994  788999999999999765

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.69  E-value=1.1e-08  Score=69.49  Aligned_cols=42  Identities=17%  Similarity=0.271  Sum_probs=37.9

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      +++++|||||+|.+.++|++||.  ++..|+|+.|.|.++.++.
T Consensus        52 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           52 WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            46889999999999999999994  7889999999999998754

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=98.69  E-value=2.9e-08  Score=85.39  Aligned_cols=50  Identities=22%  Similarity=0.349  Sum_probs=45.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|++++|||||+|.+.++|++||.  +++.|.|+.|.|.++.++...
T Consensus       134 i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~~  185 (437)
T 3pgw_S          134 MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVK  185 (437)
T ss_pred             eeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCC
Confidence            57888999999999999999999999993  788999999999999876543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.67  E-value=4.3e-08  Score=66.45  Aligned_cols=42  Identities=14%  Similarity=0.287  Sum_probs=37.5

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +++||||||+|.+.++|++||.  +++.|.|++|.|.++.++..
T Consensus        46 ~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            3689999999999999999994  78899999999999987654

>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=98.67  E-value=8.6e-09  Score=72.64  Aligned_cols=40  Identities=15%  Similarity=0.176  Sum_probs=36.4

Q ss_pred             CCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            7 SKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      +++++||+||+|++.++|.+|+  +++..++||.|.|.++..
T Consensus        67 ~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           67 DAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             TCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             CCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCh
Confidence            5789999999999999999999  478999999999998753

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=98.66  E-value=1.1e-08  Score=69.24  Aligned_cols=43  Identities=21%  Similarity=0.297  Sum_probs=38.6

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++++|||||+|.+.++|++|+.  ++..|.|+.|.|.++.++..
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           47 SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   91 (97)
T ss_dssp             HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCCc
Confidence            57899999999999999999994  78899999999999987543

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.62  E-value=3.8e-08  Score=68.66  Aligned_cols=42  Identities=14%  Similarity=0.287  Sum_probs=37.3

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      .++|||||+|.+.++|++|+.  +++.|+|++|.|.++.++...
T Consensus        62 ~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           62 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCCS
T ss_pred             CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCc
Confidence            389999999999999999994  788999999999999876543

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

Probab=98.62  E-value=2.6e-08  Score=68.51  Aligned_cols=41  Identities=17%  Similarity=0.306  Sum_probs=35.2

Q ss_pred             ccceEEEEEcCHHHHHHHHh--c--CceeCCcEEEEeeccCCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--D--THELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~--~~~i~gr~i~v~~a~~~~~~   50 (234)
                      .||||||+|++.++|++||+  +  +..|.|++|.|.++.++...
T Consensus        51 ~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~   95 (105)
T 1sjq_A           51 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK   95 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCC
Confidence            38999999999999999995  3  36899999999999876543

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.62  E-value=4.2e-08  Score=65.93  Aligned_cols=42  Identities=19%  Similarity=0.277  Sum_probs=37.3

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cC-ceeCCcEEEEeeccCCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DT-HELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~-~~i~gr~i~v~~a~~~~~~   50 (234)
                      .++|||||+|.+.++|++||+  ++ +.|+|++|.|.++.++...
T Consensus        42 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           42 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcccc
Confidence            579999999999999999994  77 8999999999999876543

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

Probab=98.60  E-value=4.9e-08  Score=66.47  Aligned_cols=40  Identities=13%  Similarity=0.235  Sum_probs=34.1

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCc--eeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTH--ELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~--~i~gr~i~v~~a~~~~   48 (234)
                      ++||||||+|++.++|.+|+.  ++.  .|.|++|.|.++.+++
T Consensus        55 ~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            468999999999999999995  333  5899999999998654

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.60  E-value=6.5e-08  Score=66.18  Aligned_cols=41  Identities=15%  Similarity=0.249  Sum_probs=35.2

Q ss_pred             ccceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCCCC
Q 026724           10 HRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      .||||||+|++.++|++|++    ++..|.|++|.|.++.++...
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~   94 (101)
T 2cq1_A           50 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELK   94 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCc
Confidence            38999999999999999995    356899999999999876543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=98.59  E-value=5.2e-08  Score=64.82  Aligned_cols=39  Identities=13%  Similarity=0.334  Sum_probs=35.4

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++||||||+|.+.++|++|+.  ++..|.|++|+|.++...
T Consensus        38 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            689999999999999999994  788999999999998643

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=1.1e-07  Score=64.69  Aligned_cols=41  Identities=24%  Similarity=0.413  Sum_probs=36.8

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .+||||||+|.+.++|++||.  +++.|.|+.|.|.++.++..
T Consensus        49 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            468999999999999999994  78899999999999987654

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.58  E-value=5.3e-08  Score=67.81  Aligned_cols=42  Identities=14%  Similarity=0.134  Sum_probs=35.9

Q ss_pred             CccceEEEEEcCHHHHHHHHh--c--CceeCCcEEEEeeccCCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--D--THELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~--~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ++||||||+|++.++|++||.  +  ...|.|++|.|.++..+...
T Consensus        60 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~~  105 (112)
T 1x4f_A           60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKL  105 (112)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSSS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcccccc
Confidence            578999999999999999995  3  34699999999999876543

>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=98.57  E-value=7.6e-08  Score=64.25  Aligned_cols=40  Identities=28%  Similarity=0.483  Sum_probs=31.6

Q ss_pred             ccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCC
Q 026724           10 HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |||||||+|++.++|+++....+.+.++.|.|.++.++..
T Consensus        47 srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           47 FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             CCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEECC----
T ss_pred             CCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEEcCCCCc
Confidence            8999999999999999655555677899999999987653

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=98.55  E-value=2.6e-07  Score=63.25  Aligned_cols=42  Identities=21%  Similarity=0.370  Sum_probs=36.9

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDF   51 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~~   51 (234)
                      .+|||||+|.+.++|++||+  +++.|.|+.|.|.++.++....
T Consensus        44 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKR   87 (103)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcccc
Confidence            47899999999999999995  7889999999999998766543

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.54  E-value=1e-07  Score=66.00  Aligned_cols=40  Identities=20%  Similarity=0.388  Sum_probs=36.1

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      +|||||+|.+.++|++||.  +++.|.|+.|.|.++.++...
T Consensus        61 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            8999999999999999994  788999999999999876543

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

Probab=98.54  E-value=4.4e-08  Score=66.89  Aligned_cols=39  Identities=13%  Similarity=0.320  Sum_probs=35.4

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++||||||+|.+.++|++|+.  ++..|+|+.|+|.++.++
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            689999999999999999994  788999999999998753

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.52  E-value=1e-07  Score=65.28  Aligned_cols=40  Identities=15%  Similarity=0.150  Sum_probs=34.1

Q ss_pred             ccceEEEEEcCHHHHHHHHh--c--CceeCCcEEEEeeccCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--D--THELGGSTVVVDRATPKED   49 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~--~~~i~gr~i~v~~a~~~~~   49 (234)
                      .||||||+|++.++|++||.  +  ...|.|++|.|.++..+..
T Consensus        51 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           51 KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR   94 (102)
T ss_dssp             SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTT
T ss_pred             CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCC
Confidence            46999999999999999995  4  3469999999999986544

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.52  E-value=8.9e-08  Score=63.89  Aligned_cols=39  Identities=15%  Similarity=0.297  Sum_probs=35.5

Q ss_pred             ceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCCCC
Q 026724           12 GIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        12 G~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |||||+|.+.++|++|+  +++..|.||+|+|.+|..+.+.
T Consensus        47 G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNREL   87 (96)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCCC
T ss_pred             CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCcce
Confidence            99999999999999999  4789999999999999876553

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

Probab=98.52  E-value=8.3e-08  Score=64.64  Aligned_cols=45  Identities=20%  Similarity=0.323  Sum_probs=38.4

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +.|+.|++   ||||+|.+.++|++||+ +++.|+|+.|.|.++.++..
T Consensus        39 ~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A           39 VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCCSCC
T ss_pred             EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCcCCC
Confidence            45677776   99999999999999995 77899999999998876544

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

Probab=98.51  E-value=1.3e-07  Score=63.01  Aligned_cols=40  Identities=18%  Similarity=0.370  Sum_probs=35.7

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      ||||||+|.+.++|++|+.  ++..|.|++|.|.++.++...
T Consensus        42 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence            7999999999999999994  678999999999999876543

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

Probab=98.50  E-value=1.4e-07  Score=63.94  Aligned_cols=38  Identities=18%  Similarity=0.397  Sum_probs=34.5

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++|||||+|.+.++|++|+.  ++..|+|+.|.|.++.++
T Consensus        56 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            58999999999999999994  688999999999998764

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.50  E-value=2.4e-07  Score=63.72  Aligned_cols=40  Identities=15%  Similarity=0.262  Sum_probs=34.3

Q ss_pred             ccceEEEEEcCHHHHHHHHh--c--CceeCCcEEEEeeccCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--D--THELGGSTVVVDRATPKED   49 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~--~~~i~gr~i~v~~a~~~~~   49 (234)
                      .||||||+|++.++|++|+.  +  ...|.|++|.|.++..+..
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccc
Confidence            48999999999999999995  3  3469999999999987654

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.49  E-value=8.5e-08  Score=65.19  Aligned_cols=41  Identities=27%  Similarity=0.362  Sum_probs=36.4

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++||||||+|.+.++|++|++  +++.|.|++|.|.++.++..
T Consensus        49 ~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            458999999999999999994  78899999999999987643

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.49  E-value=1.2e-07  Score=63.00  Aligned_cols=41  Identities=27%  Similarity=0.472  Sum_probs=35.9

Q ss_pred             ccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCCC
Q 026724           10 HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      +||||||+|.+.++|++|+...+.+.+++|.|.++.++...
T Consensus        41 ~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           41 FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCCC
T ss_pred             CCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCCCCCC
Confidence            89999999999999998876667889999999999876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.47  E-value=3.8e-07  Score=61.05  Aligned_cols=40  Identities=18%  Similarity=0.311  Sum_probs=35.6

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .++||||+|.+.++|++|+.  +++.|.|+.|.|.++.++..
T Consensus        43 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   84 (92)
T 2dgt_A           43 VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR   84 (92)
T ss_dssp             CSSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCS
T ss_pred             ECCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCC
Confidence            36699999999999999994  78899999999999987654

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.46  E-value=1.9e-07  Score=64.52  Aligned_cols=39  Identities=15%  Similarity=0.365  Sum_probs=34.8

Q ss_pred             ceEEEEEcCHHHHHHHHh--cCceeCC-----cEEEEeeccCCCCC
Q 026724           12 GIGFITFASADSVENLMV--DTHELGG-----STVVVDRATPKEDD   50 (234)
Q Consensus        12 G~aFV~F~~~e~A~~Al~--~~~~i~g-----r~i~v~~a~~~~~~   50 (234)
                      |||||+|++.++|++||+  +++.|.|     +.|.|.++.++...
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSCC
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCCC
Confidence            899999999999999995  6789999     99999999876543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.46  E-value=1.5e-06  Score=58.95  Aligned_cols=69  Identities=9%  Similarity=0.133  Sum_probs=61.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc-----CceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEE
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRF-----GRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAID  171 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~-----G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~  171 (234)
                      ..++|-+-|||..+++..|+.+.+++     |.|+.+.+..+   .+-|+|+|.|...|.+|.  +++.+|.|++|+|.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD---H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD---FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT---TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC---CCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            46788889999999999999999999     99999988865   467999999999999985  58999999999985

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.45  E-value=1.8e-07  Score=63.29  Aligned_cols=38  Identities=21%  Similarity=0.321  Sum_probs=34.8

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeC--CcEEEEeeccCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELG--GSTVVVDRATPKE   48 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~--gr~i~v~~a~~~~   48 (234)
                      ||||||+|.+.++|++|++  +++.|.  |++|.|.++.++.
T Consensus        53 ~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            8999999999999999995  788999  9999999998764

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=98.44  E-value=1.7e-07  Score=64.98  Aligned_cols=39  Identities=18%  Similarity=0.443  Sum_probs=35.3

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++|||||+|++.++|++||.  +++.|+|+.|.|.++.+..
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            68999999999999999994  7889999999999997544

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

Probab=98.44  E-value=1.9e-07  Score=64.65  Aligned_cols=39  Identities=15%  Similarity=0.291  Sum_probs=35.0

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ||||||+|.+.++|++|+.  ++..|+|+.|.|.++.++..
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK  105 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC-
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCC
Confidence            8999999999999999994  78899999999999987543

>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=98.43  E-value=1.9e-07  Score=65.30  Aligned_cols=37  Identities=8%  Similarity=0.126  Sum_probs=34.1

Q ss_pred             ccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724           10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      ++|||||+|++.++|++|+  +++..++||.|.|.++..
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL   92 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcH
Confidence            6999999999999999999  489999999999999853

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

Probab=98.43  E-value=1.3e-07  Score=63.93  Aligned_cols=40  Identities=18%  Similarity=0.375  Sum_probs=35.9

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +||||||+|.+.++|++||.  ++..|.|++|.|.++.++..
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            58999999999999999995  78899999999999977654

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.43  E-value=2.1e-07  Score=61.30  Aligned_cols=37  Identities=19%  Similarity=0.268  Sum_probs=33.1

Q ss_pred             CccceEEEEEcCHHHHHHHHh---cCceeCCcEEEEeecc
Q 026724            9 AHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRAT   45 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~---~~~~i~gr~i~v~~a~   45 (234)
                      ++||||||+|.+.++|++|+.   +++.|+|++|.|+++.
T Consensus        46 ~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           46 QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            368999999999999999995   6789999999999873

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.42  E-value=2.1e-07  Score=65.49  Aligned_cols=41  Identities=17%  Similarity=0.306  Sum_probs=35.2

Q ss_pred             ccceEEEEEcCHHHHHHHHh--c--CceeCCcEEEEeeccCCCCC
Q 026724           10 HRGIGFITFASADSVENLMV--D--THELGGSTVVVDRATPKEDD   50 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~--~~~i~gr~i~v~~a~~~~~~   50 (234)
                      .||||||+|++.++|++||+  +  +..|.|++|.|.++.++...
T Consensus        66 ~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~  110 (119)
T 2ad9_A           66 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK  110 (119)
T ss_dssp             GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCC
Confidence            48999999999999999995  3  45899999999999876543

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

Probab=98.42  E-value=2.1e-07  Score=62.73  Aligned_cols=43  Identities=16%  Similarity=0.207  Sum_probs=36.8

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++|+.++.    |||+|.+.++|++||  ++++.|.|++|.|.++.++.
T Consensus        49 ~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           49 NTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             CCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             ecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            55666554    999999999999999  47889999999999998763

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

Probab=98.42  E-value=3.9e-07  Score=60.73  Aligned_cols=39  Identities=13%  Similarity=0.327  Sum_probs=34.9

Q ss_pred             cceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++||||+|.+.++|++||.  +++.|.|+.|.|.++.++..
T Consensus        43 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A           43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            5699999999999999994  78899999999999987643

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=98.41  E-value=2.8e-07  Score=60.89  Aligned_cols=36  Identities=22%  Similarity=0.448  Sum_probs=32.0

Q ss_pred             CCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEee
Q 026724            8 KAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDR   43 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~   43 (234)
                      .++||||||+|.+.++|++|+ ++++.|.|+.|+|++
T Consensus        50 ~~~kg~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           50 NQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             CSSSSEEEEEESSHHHHHHHGGGTTCEETTEECEEEC
T ss_pred             cCCCcEEEEEcCCHHHHHHHHhcCCCEECCeEEEEeC
Confidence            356999999999999999999 468899999999974

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.40  E-value=2.3e-07  Score=64.56  Aligned_cols=39  Identities=5%  Similarity=-0.008  Sum_probs=35.3

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++||||||+|.+.++|++||.  ++..|.|++|.|.++...
T Consensus        44 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            478999999999999999994  788999999999998754

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=98.39  E-value=3.6e-07  Score=67.72  Aligned_cols=42  Identities=14%  Similarity=0.166  Sum_probs=36.2

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCC--cEEEEeeccCCCC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGG--STVVVDRATPKED   49 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~g--r~i~v~~a~~~~~   49 (234)
                      +.++|||||+|++.++|++|++  ++..|.+  ++|+|+++.++..
T Consensus        81 k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           81 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             SSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            3478999999999999999995  7888965  9999999987643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.38  E-value=1.1e-05  Score=54.17  Aligned_cols=76  Identities=32%  Similarity=0.374  Sum_probs=64.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhh-----cCceeEEEeecCCCCcceEEEEEcChHHHHHHHhc-CCccCCeEeEEEe
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSR-----FGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR-SHEICGQQVAIDS  172 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~-----~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~  172 (234)
                      ....+|.|.|||..++++.|+-+|+.     =|+|..+....     .-|+|+|.+.+.|++.|.+ .|.|++..|.|.-
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-----~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P   80 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-----CGGVLTFREPADAERVLAQADHELHGAQLSLRP   80 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-----TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-----CcEEEEEcChHHHHHHhcCCcceecCeEEEEEc
Confidence            35689999999999999999999976     26788887753     5699999999999999976 8999999999987


Q ss_pred             CCCCCCC
Q 026724          173 ATPLDDA  179 (234)
Q Consensus       173 a~~~~~~  179 (234)
                      ..++...
T Consensus        81 ~~~~~~~   87 (104)
T 2dhx_A           81 APPRAPA   87 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCcc
Confidence            6665543

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.30  E-value=7.5e-07  Score=62.05  Aligned_cols=38  Identities=11%  Similarity=0.220  Sum_probs=33.0

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCcee-----CCcEEEEeeccCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHEL-----GGSTVVVDRATPK   47 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i-----~gr~i~v~~a~~~   47 (234)
                      +||||||+|++.++|++|++  +++.|     .+++|.|.++...
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV  106 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccC
Confidence            48999999999999999994  67777     6899999998644

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.28  E-value=9.5e-07  Score=62.98  Aligned_cols=41  Identities=12%  Similarity=0.191  Sum_probs=35.6

Q ss_pred             Cccce-EEEEEcCHHHHHHHH--hcCceeCC--cEEEEeeccCCCC
Q 026724            9 AHRGI-GFITFASADSVENLM--VDTHELGG--STVVVDRATPKED   49 (234)
Q Consensus         9 ~srG~-aFV~F~~~e~A~~Al--~~~~~i~g--r~i~v~~a~~~~~   49 (234)
                      +++|| |||+|.+.++|++|+  +++..|.+  +.|+|+++.++.-
T Consensus        63 ~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           63 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            35788 999999999999999  47889988  8999999987653

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=98.15  E-value=1.8e-06  Score=60.31  Aligned_cols=37  Identities=16%  Similarity=0.390  Sum_probs=30.1

Q ss_pred             ceEEEEEcCHHHHHHHHh--cCceeCCcE-----EEEeeccCCC
Q 026724           12 GIGFITFASADSVENLMV--DTHELGGST-----VVVDRATPKE   48 (234)
Q Consensus        12 G~aFV~F~~~e~A~~Al~--~~~~i~gr~-----i~v~~a~~~~   48 (234)
                      |||||+|++.++|++||+  ++..|+|+.     |+|..+.++.
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~~   95 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRS   95 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC---
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCCC
Confidence            999999999999999994  788999988     7777665543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.14  E-value=3e-06  Score=60.01  Aligned_cols=38  Identities=18%  Similarity=0.322  Sum_probs=33.4

Q ss_pred             ce-EEEEEcCHHHHHHHHh--cCceeCC--cEEEEeeccCCCC
Q 026724           12 GI-GFITFASADSVENLMV--DTHELGG--STVVVDRATPKED   49 (234)
Q Consensus        12 G~-aFV~F~~~e~A~~Al~--~~~~i~g--r~i~v~~a~~~~~   49 (234)
                      || |||+|++.++|++|++  ++..|.|  ++|+|.+|.++..
T Consensus        62 Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           62 GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            86 9999999999999994  7889987  6999999987653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.93  E-value=1.3e-05  Score=52.92  Aligned_cols=35  Identities=23%  Similarity=0.386  Sum_probs=31.6

Q ss_pred             eEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCC
Q 026724           13 IGFITFASADSVENLM-VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus        13 ~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~   47 (234)
                      .+||+|.+.++|.+|| +++..++||.|+|+++.+.
T Consensus        51 ~~fVtF~d~~sAlaAi~mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           51 KMWVTFLEGSSALNVLSLNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             SEEEEESSHHHHHHGGGGTTCEETTEEEEEEECCCS
T ss_pred             CEEEEECChHHHHHHHhcCCeEeCCeEEEEEeCCCC
Confidence            3899999999999999 5888999999999988753

>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=97.70  E-value=0.00021  Score=48.23  Aligned_cols=75  Identities=11%  Similarity=0.104  Sum_probs=59.8

Q ss_pred             CCCEEEEeCCCCCC-C----HHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724          100 IGKKIFVGRLPQEA-T----AEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus       100 ~~~~l~v~nl~~~~-~----~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      -.++|+|.||+.++ .    .+.++++|..|+++......+.   -.-..|.|.+.++|.+|-  ++...++|+.|+|-+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS---FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YF   80 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS---FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT---TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc---ceEEEEEeCChHHHHHHHHHhccceecCceeEEEe
Confidence            35789999998866 2    2578999999999888766653   234689999999999995  456689999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      +++..
T Consensus        81 gq~~~   85 (104)
T 1wey_A           81 AQTLH   85 (104)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            98543

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.66  E-value=0.00021  Score=47.44  Aligned_cols=55  Identities=22%  Similarity=0.343  Sum_probs=44.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      ......++| ++|.++...||.++|+.||.| .|..+.+    .-|||.|.+++.|..|+.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD----TsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD----TSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET----TEEEEECSCHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC----CeEEEEecCHHHHHHHHH
Confidence            334556667 999999999999999999954 4666655    379999999999988874

>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=97.55  E-value=4.9e-05  Score=50.46  Aligned_cols=32  Identities=25%  Similarity=0.430  Sum_probs=29.4

Q ss_pred             EEEEEcCHHHHHHHH-hcCceeCCcEEEEeecc
Q 026724           14 GFITFASADSVENLM-VDTHELGGSTVVVDRAT   45 (234)
Q Consensus        14 aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~   45 (234)
                      +||+|.+.++|.+|| +++..++||.|+|++..
T Consensus        61 ~fVtF~d~~sAl~AI~ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           61 MLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             EEEEEcChHHHHHHHhcCCeeeCCeEEEEeccC
Confidence            999999999999999 58889999999998754

>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=97.30  E-value=0.0002  Score=59.40  Aligned_cols=36  Identities=14%  Similarity=0.312  Sum_probs=28.6

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCcee---CCc--EEEEeecc
Q 026724           10 HRGIGFITFASADSVENLMV--DTHEL---GGS--TVVVDRAT   45 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i---~gr--~i~v~~a~   45 (234)
                      +||||||+|++.++|++||+  |+..+   .|+  +|.|.++.
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            78999999999999999995  66655   345  57777763

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.30  E-value=0.001  Score=46.07  Aligned_cols=72  Identities=13%  Similarity=0.198  Sum_probs=56.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh-cCCccCC-eEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR-RSHEICG-QQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~g-~~i~v~~a  173 (234)
                      ......|.|-+.|... ...|..+|++||.|.+.....   ...+-.|.|.+..+|++||. |+..|++ -.|-|...
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~---~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN---TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS---SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC---CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            3346788999999886 556778899999999887632   35789999999999999995 7777775 56677664

>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=97.30  E-value=0.00041  Score=46.23  Aligned_cols=51  Identities=22%  Similarity=0.358  Sum_probs=42.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      ..++| ++|.++...||.++|+.||. ..|.++.+    .-|||.|.+++.|..|+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidD----TsAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD----TSAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEET----TEEEEEEEEECHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcC----CeEEEEecCHHHHHHHHH
Confidence            34566 99999999999999999994 45666665    379999999999998874

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

Probab=97.17  E-value=0.00025  Score=53.28  Aligned_cols=25  Identities=16%  Similarity=0.118  Sum_probs=22.9

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHhc
Q 026724            6 GSKAHRGIGFITFASADSVENLMVD   30 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~~   30 (234)
                      .|++++|||||+|.+.++|++||+.
T Consensus       124 ~~g~~kG~afV~F~~~~~A~~Ai~~  148 (177)
T 2f3j_A          124 RSGRSLGTADVHFERRADALKAMKQ  148 (177)
T ss_dssp             TTSSCSCCEEEEESCHHHHHHHHHH
T ss_pred             CCCCEeeEEEEEeCCHHHHHHHHHH
Confidence            4689999999999999999999975

>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=96.88  E-value=0.0045  Score=40.85  Aligned_cols=60  Identities=13%  Similarity=0.093  Sum_probs=46.3

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC-C--CcceEEEEEcChHHHHHHHh--cCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT-G--HRGFGFVTFAEEVVADRVSR--RSH  161 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~-~--~~g~afV~f~~~~~a~~A~~--~~~  161 (234)
                      .+|.|++||+++||+++.+.++.+..+.....+  +.+ +  .-.-|+|.|.+.+++..-..  +++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~   68 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Confidence            579999999999999999999998877666665  211 2  34669999999888777653  455

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.82  E-value=0.0016  Score=43.78  Aligned_cols=34  Identities=26%  Similarity=0.452  Sum_probs=30.2

Q ss_pred             ceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeecc
Q 026724           12 GIGFITFASADSVENLMVD-THELGGSTVVVDRAT   45 (234)
Q Consensus        12 G~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~   45 (234)
                      +-|+|+|.+.+.|++.|.+ .|.|.+.+|.|....
T Consensus        48 ~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A           48 CGGVLTFREPADAERVLAQADHELHGAQLSLRPAP   82 (104)
T ss_dssp             TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEECC
T ss_pred             CcEEEEEcChHHHHHHhcCCcceecCeEEEEEcCC
Confidence            5689999999999999987 999999999997544

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=96.56  E-value=0.0011  Score=47.97  Aligned_cols=21  Identities=14%  Similarity=0.438  Sum_probs=19.6

Q ss_pred             ccceEEEEEcCHHHHHHHHhc
Q 026724           10 HRGIGFITFASADSVENLMVD   30 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~~   30 (234)
                      +||||||+|.+.++|++||..
T Consensus       109 ~~g~afV~f~~~~~a~~A~~~  129 (150)
T 2i2y_A          109 PPGFAFVEFEDPRDAADAVRE  129 (150)
T ss_dssp             SCSEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEEECCHHHHHHHHHH
Confidence            699999999999999999964

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

Probab=96.56  E-value=0.0015  Score=51.32  Aligned_cols=22  Identities=18%  Similarity=0.297  Sum_probs=19.8

Q ss_pred             CccceEEEEEcCHHHHHHHHhc
Q 026724            9 AHRGIGFITFASADSVENLMVD   30 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~~   30 (234)
                      .+||||||+|.+.++|+.|++.
T Consensus       177 ~~kG~AFV~F~~~~~Ae~A~~a  198 (240)
T 3u1l_A          177 ESKNCGFVKFKYQANAEFAKEA  198 (240)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHH
Confidence            4799999999999999999953

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.50  E-value=0.0015  Score=56.09  Aligned_cols=55  Identities=15%  Similarity=0.396  Sum_probs=41.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      .+.|+|. .|..+++.+|.++|++||.|.++.+-++  ..-|+.|+|.+.+++.+++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CCeEEEEEeCCHHHHHHHHh
Confidence            4689997 7999999999999999999999877654  34799999999999887764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.41  E-value=0.0057  Score=42.96  Aligned_cols=73  Identities=21%  Similarity=0.268  Sum_probs=53.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEeec-----------CCC-----CcceEEEEEcChHHHHHHH-hcCCc
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPK-----------RTG-----HRGFGFVTFAEEVVADRVS-RRSHE  162 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~-----------~~~-----~~g~afV~f~~~~~a~~A~-~~~~~  162 (234)
                      ...|.|-+.|.+.+.. +.+.|++||.|.+ +.+.+           ...     ...+-.|+|++..+|.+|| .++..
T Consensus         7 e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            4567788897776654 5677999999876 22211           000     1467799999999999999 58899


Q ss_pred             cCCeEeEEEeCC
Q 026724          163 ICGQQVAIDSAT  174 (234)
Q Consensus       163 ~~g~~i~v~~a~  174 (234)
                      |+|..|-|....
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988887664

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.31  E-value=0.02  Score=38.03  Aligned_cols=58  Identities=12%  Similarity=0.011  Sum_probs=41.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cC-CC--CcceEEEEEcChHHHHHHH
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KR-TG--HRGFGFVTFAEEVVADRVS  157 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~-~~--~~g~afV~f~~~~~a~~A~  157 (234)
                      .+-+|.|+.||+.+||+++.+.++.+-.+.....+  +. .+  .-.-|+|.|.+.++...-.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~   70 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFR   70 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHH
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHH
Confidence            46789999999999999988877765444333332  11 11  2356899999998877765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=94.88  E-value=0.038  Score=37.52  Aligned_cols=33  Identities=9%  Similarity=0.245  Sum_probs=28.8

Q ss_pred             ceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeec
Q 026724           12 GIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (234)
Q Consensus        12 G~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a   44 (234)
                      +=|+|+|+|...|-+|.+  ++.+|.|++|+|.-.
T Consensus        63 ~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           63 NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            459999999999999984  799999999999643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.32  E-value=0.056  Score=37.60  Aligned_cols=33  Identities=18%  Similarity=0.151  Sum_probs=26.8

Q ss_pred             eEEEEEcC-HHHHHHHHh----cCceeCCcEEEEeecc
Q 026724           13 IGFITFAS-ADSVENLMV----DTHELGGSTVVVDRAT   45 (234)
Q Consensus        13 ~aFV~F~~-~e~A~~Al~----~~~~i~gr~i~v~~a~   45 (234)
                      .|||.|.+ .++|.+|+.    ++..|.+..++++...
T Consensus        57 tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           57 EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            49999999 889999994    2568899888887654

>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=89.65  E-value=1.1  Score=38.96  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=42.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      ....++|+ +|..+...+|.++|+.||.| +|.++.+    ..|||.|.+.+.|..++.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd----t~a~V~~~~~~~a~~~l~  491 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD----TSAFVSLSQPEQVQIAVN  491 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS----SEEEEECSCHHHHHHHHH
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC----CeEEEEECCHHHHHHHHH
Confidence            34567776 89999999999999999954 5555543    479999999999998874

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=84.28  E-value=1.2  Score=31.09  Aligned_cols=35  Identities=17%  Similarity=0.113  Sum_probs=29.8

Q ss_pred             cceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeecc
Q 026724           11 RGIGFITFASADSVENLM-VDTHELGGSTVVVDRAT   45 (234)
Q Consensus        11 rG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~   45 (234)
                      ..+-.|+|.+..+|++|| +|+..|.|.-|-|....
T Consensus        62 ~NWikItYds~~~A~rAL~~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           62 NSWTKITYDNPASAVDALLENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TTEEEEEBSSHHHHHHHHTTTTCEETTEECEEEECC
T ss_pred             CcEEEEEcCCHHHHHHHHHhCCeEeCcEEEEEEECC
Confidence            457799999999999999 58999999887777654

---

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	234
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	8e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	8e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.003
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.001
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	8e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	8e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	9e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.003
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.003
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003

>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 = 63.9 bits (155), Expect = 5e-14
 Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 4/92 (4%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL---DVYVPKRTGHRGFGFVTFAE 149
           R +  +   +K+F+G L  E T E LR Y+ ++G++     +  P     RGFGFVTF+ 
Sbjct: 12  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 71

Query: 150 EVVADR-VSRRSHEICGQQVAIDSATPLDDAG 180
               D  ++ R H I G+ V    A   +++G
Sbjct: 72  MAEVDAAMAARPHSIDGRVVEPKRAVAREESG 103

>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 = 39.3 bits (91), Expect = 4e-05
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
           + +D  SK  RG GF+TF+S   V+  M    H + G  V   RA  +E+
Sbjct: 52  VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE 101

>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 = 62.3 bits (151), Expect = 8e-14
 Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFG---RILDVYVPKRTGHRGFGFVTFAEEVVADR-VSR 158
           KIFVG L  +   E +R YF  FG    I      K    RGF F+TF EE    + + +
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 159 RSHEICGQQVAIDSA 173
           + H +   +  I  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 62.3 bits (151), Expect = 1e-13
 Identities = 26/78 (33%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVS 157
              + V  LP + T +DL+ YFS FG +L V V    K    +GFGFV F E     +V 
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 158 RRSHEICGQQVAIDSATP 175
            + H I G+         
Sbjct: 68  SQRHMIDGRWCDCKLPNS 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.5 bits (110), Expect = 8e-08
 Identities = 10/49 (20%), Positives = 19/49 (38%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED 49
          + KD  +   +G GF+ F   ++   +M   H + G          K+ 
Sbjct: 40 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS 88

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.5 bits (149), Expect = 3e-13
 Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 7/87 (8%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---TG-HRGFGFVTFAEEV 151
             ++   KI V  +P +A   ++R  FS FG +  V +PK+   TG HRGFGFV F  + 
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 152 VADRVSRR---SHEICGQQVAIDSATP 175
            A +       S  + G+++ ++ A  
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 36.1 bits (83), Expect = 5e-04
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVE---NLMVDTHELGGSTVVVDRATPKE 48
            K  G+ AHRG GF+ F +    +   N +  +  L G  +V++ A  + 
Sbjct: 41 PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 58.9 bits (142), Expect = 3e-12
 Identities = 28/81 (34%), Positives = 46/81 (56%), Gaps = 2/81 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
             +FVGR   + T ++LR +FS++G ++DV++PK    R F FVTFA++ +A  +     
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCGEDL 63

Query: 162 EICGQQVAIDSATPLDDAGPS 182
            I G  V I +A P  ++   
Sbjct: 64  IIKGISVHISNAEPKHNSNSG 84

>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 = 39.6 bits (92), Expect = 3e-05
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 10 HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           R   F+TFA     ++L  +   + G +V +  A PK +        S G
Sbjct: 41 FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNSG---PSSG 88

>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 = 59.3 bits (143), Expect = 3e-12
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH 161
           + +++  LP + TAE++   F ++G I  + V      RG  +V + +   A        
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 162 --EICGQQVAIDSATP 175
              +C + + +     
Sbjct: 68  GFNVCNRYLVVLYYNA 83

>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 = 57.7 bits (139), Expect = 6e-12
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADR-VS 157
           +K+F+G L  E T E LR +F ++G + D  V     T   RGFGFVT+A     D  ++
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 158 RRSHEICGQQVAIDSA 173
            R H++ G+ V    A
Sbjct: 67  ARPHKVDGRVVEPKRA 82

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.3 bits (138), Expect = 8e-12
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFG--RILDVYVPKRTG-HRGFGFVTFAEEVVADR-VSR 158
           K+F+G L  + T E LR YF +FG  +   V     T   RGFGFVTF ++   D+ +++
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 159 RSHEICGQQVAIDSA 173
             HE+  + +    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 54.5 bits (131), Expect = 7e-11
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVTFAEEVVADRVSRR 159
            ++VG L  + T   L   FS  G IL + V +        G+ +V F +   A+R    
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 160 --SHEICGQQVAIDSAT 174
                I G+ V I  + 
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 54.7 bits (131), Expect = 9e-11
 Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 11/93 (11%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-----HRGFGFVTFAEEVVADRVS 157
           ++F+G +P+    E++    ++    +   +   +      +RGF FV +     A    
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 158 R----RSHEICGQQVAIDSATPLDDAGPSQNFM 186
           R       ++ G Q+A+D A P  D    ++ M
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEID--VDEDVM 93

>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 = 38.5 bits (89), Expect = 8e-05
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKED 49
                   +RG  F+ + S  +       LM    +L G  + VD A P+ D
Sbjct: 35 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 87

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 4/82 (4%)

Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA-EEVVA 153
           +R  + +F  +L       DL  +FS  G++ DV +         +G  +V F   + V 
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 154 DRVSRRSHEICGQQVAIDSATP 175
             +      + G  + + ++  
Sbjct: 75  LAIGLTGQRLLGVPIIVQASQA 96

>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 = 53.8 bits (129), Expect = 1e-10
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 4/76 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--TGHRGFGFVTFAEEVVADRVSRRS 160
           K+ V  L    +  D++  F+ FG +    V         G   V F  +  A +  ++ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 161 H--EICGQQVAIDSAT 174
           +   + G+ + I   T
Sbjct: 62  NGVPLDGRPMNIQLVT 77

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 2e-10
 Identities = 16/73 (21%), Positives = 31/73 (42%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHE 162
           K+++G L    TA+DLR+ F      L   V  ++G+    +      + A        E
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 163 ICGQQVAIDSATP 175
           + G+ + +D +  
Sbjct: 63  LHGKIMEVDYSVS 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 2e-10
 Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 4/70 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADR-VSR 158
           K+F+G L  + T +DL+ YFS+FG ++D  +   P     RGFGFV F E    D+ + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 159 RSHEICGQQV 168
           + H++ G+ +
Sbjct: 61  KEHKLNGKVI 70

>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 = 52.8 bits (126), Expect = 4e-10
 Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG----HRGFGFVTFAEEVVADRV--S 157
           IF+G L  E   + L   FS FG IL      R       +G+ F+ FA    +D    +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 158 RRSHEICGQQVAIDSATPLDDAG 180
                +C + + +  A   D  G
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSKG 83

>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 = 52.2 bits (125), Expect = 9e-10
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 98  QRIGKKIFVGRLPQEATAE-DLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV 156
           + +  ++F+G L      + D+   FS++G+I+   V     H+GF FV +  E  A   
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAA 66

Query: 157 SRR--SHEICGQQVAIDSATP 175
                   I GQ + I+ A  
Sbjct: 67  VAGEDGRMIAGQVLDINLAAE 87

>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 = 51.5 bits (123), Expect = 2e-09
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRS 160
              ++ G +    T + +R+ FS FG+I+++ V      +G+ FV F+    A       
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---EKGYSFVRFSTHESAAHAIVSV 74

Query: 161 H--EICGQQVAIDSATP 175
           +   I G  V       
Sbjct: 75  NGTTIEGHVVKCYWGKE 91

>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 = 50.4 bits (120), Expect = 3e-09
 Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGHRGFGFVTFAEEVV 152
           S+      ++V  LP+  T ++L + FS++GRI+    +        RG GF+ F + + 
Sbjct: 1   SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 60

Query: 153 ADRV 156
           A+  
Sbjct: 61  AEEA 64

>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 = 50.4 bits (120), Expect = 3e-09
 Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV---YVPKRTGHRGFGFVTFAEEVVADRV--S 157
           K+F+G LP     + ++   + FG +              +G+ F  + +  V D+    
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 158 RRSHEICGQQVAIDSATP 175
               ++  +++ +  A+ 
Sbjct: 63  LNGMQLGDKKLLVQRASV 80

>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 = 33.5 bits (76), Expect = 0.003
 Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 2/40 (5%)

Query: 10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
           +G  F  +   +  +  +  ++  +LG   ++V RA+  
Sbjct: 42 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 81

>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 = 50.0 bits (119), Expect = 4e-09
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL---DVYVPKRTGHRGFGFVTFAEE 150
           GES +     ++V  LP+  T + L   F ++G I+    +        RG  FV + + 
Sbjct: 1   GESIK--DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 58

Query: 151 VVADR 155
             A  
Sbjct: 59  EEAQE 63

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.0 bits (119), Expect = 5e-09
 Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVA 153
           GE +     ++FVG LP + T E++R+ F ++G+  +V++ K    +GFGF+      +A
Sbjct: 1   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLA 57

Query: 154 DRVSRR--SHEICGQQVAIDSATP 175
           +       +  + G+Q+ +  A  
Sbjct: 58  EIAKVELDNMPLRGKQLRVRFACH 81

>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 = 49.6 bits (118), Expect = 6e-09
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTGHRGFGFVTFAEEVVADRVSRR 159
            + V  LPQ+ T  +L   F   G I    +    K     G+ FV F  E+ + R  + 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 160 --SHEICGQQVAIDSATP 175
                +  +++ +  A P
Sbjct: 64  LNGITVRNKRLKVSYARP 81

>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 = 49.3 bits (117), Expect = 7e-09
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 8/80 (10%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP------KRTGHRGFGFVTFAEEVVADRVS 157
           +F+  L    T E L+  FS+ G I    +             GFGFV + +   A +  
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 158 RR--SHEICGQQVAIDSATP 175
           ++   H + G ++ +  +  
Sbjct: 61  KQLQGHTVDGHKLEVRISER 80

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRIL---DVYVPKRTGHRGFGFVTFAEEVVADRV-SR 158
           KIFVG L    T ED++ YF +FG++     ++      HRGFGFVTF  E + ++V   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 159 RSHEICGQQVAIDSA 173
             HEI  + V    A
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 48.5 bits (115), Expect = 2e-08
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR--S 160
           +I+VG LP +   +D+   F ++G I D+ +  R G   F FV F +   A+        
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 75

Query: 161 HEICGQQVAIDSATP 175
           ++  G ++ ++    
Sbjct: 76  YDYDGYRLRVEFPRS 90

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 3/82 (3%)

Query: 97  SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPKRTGHRGFGFVTFAEEVVADR 155
           S+   K++ V  +P      DLR+ F +FG+ILD   +    G +GFGFVTF     ADR
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 156 VSRR--SHEICGQQVAIDSATP 175
              +     + G+++ +++AT 
Sbjct: 67  AREKLHGTVVEGRKIEVNNATA 88

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 2e-08
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRTGHRGFGFVTFAEEVVADRVSRRS 160
           + ++VG L ++ T   + + FS+ G       + + T +  + FV F E   A       
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 161 H--EICGQQVAIDSATP 175
           +  +I G++V ++ AT 
Sbjct: 69  NGRKILGKEVKVNWATT 85

>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 = 48.0 bits (114), Expect = 2e-08
 Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 5/86 (5%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEV 151
           E   +    ++VG L    T E +   FS+ G I  + +     +    GF FV +    
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 152 VADRVSRRSH--EICGQQVAIDSATP 175
            A+   R  +   +  + +  D    
Sbjct: 61  DAENAMRYINGTRLDDRIIRTDWDAG 86

>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 = 47.4 bits (112), Expect = 3e-08
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADR-VS 157
           KKIFVG + ++     LR YF ++G+I  + +         RGF FVTF +    D+ V 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 158 RRSHEICGQQVAIDSA 173
           ++ H + G    +  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 47.7 bits (113), Expect = 3e-08
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRV-- 156
           + ++VG L +E   + L   F  FG I D+ +    +   HRGF FV F     A     
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 157 SRRSHEICGQQVAIDSATP 175
           +    E+ G+ + ++ A P
Sbjct: 66  NMNESELFGRTIRVNLAKP 84

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 47.7 bits (113), Expect = 3e-08
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 99  RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV-- 156
           R  + +    L    T ++L+  F     I  V    +   +G  ++ F  E  A++   
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK--SKGIAYIEFKSEADAEKNLE 71

Query: 157 SRRSHEICGQQVAIDSATP 175
            ++  EI G+ V++     
Sbjct: 72  EKQGAEIDGRSVSLYYTGE 90

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 4e-08
 Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 102 KKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV- 156
             I++  L ++   ++L++     FSRFG+ILD+ V +    RG  FV F E   A    
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 157 -SRRSHEICGQQVAIDSATPLDDA 179
            S +      + + I  A    D 
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDI 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 = 47.1 bits (111), Expect = 4e-08
 Identities = 10/79 (12%), Positives = 22/79 (27%), Gaps = 5/79 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRIL-----DVYVPKRTGHRGFGFVTFAEEVVADRVS 157
            +++   P   T  ++R        +             +    +  VT  E+       
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 158 RRSHEICGQQVAIDSATPL 176
               +I G  +    + PL
Sbjct: 63  LNGLKIEGYTLVTKVSNPL 81

>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 = 46.9 bits (111), Expect = 6e-08
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKRTGHRGFGFVTFAEEVV 152
           S +     ++VG L ++ +   L   F + G +++           H+G+GFV F  E  
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 153 ADRV--SRRSHEICGQQVAIDSATP 175
           AD         ++ G+ + ++ A+ 
Sbjct: 64  ADYAIKIMDMIKLYGKPIRVNKASA 88

>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 = 46.4 bits (109), Expect = 6e-08
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEV-VADRVSRRS 160
            + V  LP+      + +YF   G I+ V V      +  F  + FA        +++  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 61

Query: 161 HEICGQQVAIDSAT 174
             +   ++ +   T
Sbjct: 62  KVVGQNEIIVSHLT 75

>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 = 46.6 bits (110), Expect = 7e-08
 Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRR-- 159
           K ++V  L    + E + + F+         V K    R + FV F+    A    +   
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALN 65

Query: 160 SHEICGQQVAIDSATPLD 177
              + G  + +  A P+D
Sbjct: 66  GKVLDGSPIEVTLAKPVD 83

>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 = 46.6 bits (110), Expect = 9e-08
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 96  SSQRIG-KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-TGHRGFGFVTFAEEVVA 153
           S ++ G   IF+  L +    + L   FS FG IL   V     G +G+GFV F  +  A
Sbjct: 2   SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 154 DRVSRR--SHEICGQQVAIDSATP 175
           +R   +     +  ++V +     
Sbjct: 62  ERAIEKMNGMLLNDRKVFVGRFKS 85

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (113), Expect = 1e-07
 Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV--YVPKRTG-HRGFGFVTFAEEVVADRVSR 158
           +K+F+G L  E T E LR +F ++G + D        T   RGFGFVT+A     D    
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 159 RSHEICGQQV 168
                   +V
Sbjct: 67  ARPHKVDGRV 76

>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 = 45.4 bits (106), Expect = 9e-07
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGH---RGFGFVTFAEEVVADR-VS 157
           KKIFVG + ++     LR YF ++G+I  + +    G    RGF FVTF +    D+ V 
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

Query: 158 RRSHEICGQQVAIDSATP 175
           ++ H + G    +  A  
Sbjct: 158 QKYHTVNGHNCEVRKALS 175

>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 = 41.1 bits (95), Expect = 3e-05
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED 49
           +  D+GS   RG  F+TF   DSV+ +++   H + G    V +A  K++
Sbjct: 129 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 178

>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 = 45.9 bits (108), Expect = 2e-07
 Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI---LDVYVPKRTGHRGFGFVTFAEEVVADR-VS 157
            KIFVG LP   T   LR+YF  FG I   + +   +    RG+GFVT A+   A+R   
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 158 RRSHEICGQQVAIDSATP 175
             +  I G++  ++ A  
Sbjct: 71  DPNPIIDGRKANVNLAYL 88

>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 = 45.9 bits (108), Expect = 2e-07
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 9/78 (11%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-------RTG-HRGFGFVTFAEEVVA 153
           ++++VG +P   T E +  +F+   R+  +           +    + F F+ F      
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 154 DR-VSRRSHEICGQQVAI 170
            + ++       GQ + I
Sbjct: 62  TQAMAFDGIIFQGQSLKI 79

>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 = 44.4 bits (104), Expect = 5e-07
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 11/90 (12%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADR-- 155
           GK +F+  L  ++  E L     +FG +  V V   P     +G  F  F  +  A +  
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 156 ------VSRRSHEICGQQVAIDSATPLDDA 179
                       ++ G+Q+ +D A   D+A
Sbjct: 68  AAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRI---LDVYVPKRTGHRGFGFVTFAEEVVADRVSRR 159
            + V  LPQ  T E+ R  F   G I     V         G+GFV + +   A++    
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 160 --SHEICGQQVAIDSATP 175
                +  + + +  A P
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 101 GKKIFVGRLPQEATAED-LRRYFSRFGRILDVYVPKRTG----HRGFGFVTFAEEVVADR 155
           G++I +  L  E   E+ LR  F  FG I  + +P        +    F+ F  +  A+R
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 156 -VSRRSHEICGQQVAIDSATP 175
            +      +  +++++  A  
Sbjct: 64  ALQMNRSLLGNREISVSLADK 84

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 83  LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RTGH-R 140
           +Y +P +     +  +     + +     E   E       ++G + ++ V      H  
Sbjct: 9   IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLV 68

Query: 141 GFGFVTFAEEVVADRVSRRSH--EICGQQVAID 171
           G  +V F  E  A++     +     GQ +  +
Sbjct: 69  GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRIL---DVYVPKRTGHRGFGFVTFAEEVVADRV--S 157
           K+FVG L  +   + L + FS++G+I     V   +    RGFGFVTF     A     +
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 158 RRSHEICGQQVAIDSATP 175
                + G+Q+ +D A  
Sbjct: 67  MNGKSVDGRQIRVDQAGK 84

>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 = 35.1 bits (80), Expect = 0.001
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD 50
          + KD+ ++  RG GF+TF + D  ++ M+  +   + G  + VD+A    D+
Sbjct: 37 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 8/97 (8%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV---YVPKRTGHRGFGFVTFAEE 150
           G S      ++FV  L   ++ EDL + FS +G + ++           +GF FVTF   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 151 VVADRVSRR--SHEICGQQVAIDSATPLDDA---GPS 182
             A +           G+ + +  +T   +A   GPS
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---TGHRGFGFVTFAEEVVADRVSR 158
             I V  L ++    DL+  F  FG I  +Y+ K       +GF F++F     A R   
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 159 R--SHEICGQQVAIDSATP 175
                      + ++ A P
Sbjct: 69  GVSGFGYDHLILNVEWAKP 87

>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 = 41.6 bits (97), Expect = 4e-06
 Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 5/75 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADRVS 157
              + V  L    T  DLR  FS++G I DV +    +    RGF FV F     A    
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 158 RR--SHEICGQQVAI 170
            R    E+ G+++ +
Sbjct: 69  ERANGMELDGRRIRV 83

>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 = 41.2 bits (96), Expect = 6e-06
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 97  SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV 156
           + R G  ++V       T   LR  FS FG I+D+ +      R   FVT+ +   AD+ 
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP---PRNCAFVTYEKMESADQA 55

Query: 157 SRRSH--EICGQQVAIDSATP 175
               +  ++   Q+ ++ A  
Sbjct: 56  VAELNGTQVESVQLKVNIARK 76

>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 = 41.2 bits (96), Expect = 7e-06
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFG---RILDVYVPKRTGHRGFGFVTFAEEVVADRVS 157
           G  +FV  + +EA  ++++  F  +G    I      +    +G+  V +     A    
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 158 RRSH--EICGQQVAIDSATP 175
              +  EI GQ + +D    
Sbjct: 67  EALNGAEIMGQTIQVDWCFV 86

>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 = 41.3 bits (96), Expect = 7e-06
 Identities = 13/88 (14%), Positives = 27/88 (30%), Gaps = 13/88 (14%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV-----------PKRTGHRGFGFVTFAE 149
              I+V  L    T +DL  +F + G +                 +    +G   V++ +
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 150 EVVADRVSRR--SHEICGQQVAIDSATP 175
              A          +  G ++ +  A  
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 41.2 bits (96), Expect = 9e-06
 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
            +I V  L    T + L + FS+FG +L +    +  ++    + +A+ V A  
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQH 60

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVTFAEEVVADRVS 157
           G  +F+  LPQE   +DL + F  FG ++   V         + FGFV++   V A    
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 158 RR--SHEICGQQVAIDSATPLDDA 179
           +     +I  +++ +      +D+
Sbjct: 78  QSMNGFQIGMKRLKVQLKRSKNDS 101

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 3/65 (4%)

Query: 116 EDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQVAIDSA 173
           EDLR   S+FG+I  + +  R    G   V+F +   AD   +        G+Q+   + 
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRH-PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

Query: 174 TPLDD 178
               D
Sbjct: 93  DGTTD 97

>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 = 38.9 bits (90), Expect = 4e-05
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKRTGHRGFGFVTFAEEVVADR-VSR 158
           + +++   P +AT +D++ +    G++L+  +        +G  FV F     A + V  
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 66

Query: 159 RSHEICGQQVAIDSA 173
              +     + I   
Sbjct: 67  PGQKYKETDLLILFK 81

>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 = 39.0 bits (90), Expect = 5e-05
 Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 5/93 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRIL---DVYVPKRTGHRGFGFVTFAEEVVADRVSR 158
           + +FVG +P EAT E L+  FS  G ++    VY  +    +G+GF  + ++  A    R
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 159 R--SHEICGQQVAIDSATPLDDAGPSQNFMMNA 189
                E  G+ + +D+A    +    ++    A
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>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 = 38.9 bits (90), Expect = 6e-05
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 10/99 (10%)

Query: 94  GESSQRI----GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG---HRGFGFVT 146
           G S  R+        F+G LP + T E ++ +F            + +     +GFG+  
Sbjct: 4   GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE 63

Query: 147 FAEEVVADR-VSRRSHEICGQQVAIDSATPLDDA--GPS 182
           F +       +S     +  +++ +D A    D   GPS
Sbjct: 64  FEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPS 102

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

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 = 38.7 bits (89), Expect = 8e-05
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 4/88 (4%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFA 148
            R  S    G  +++  LP EA  + +  +F +   + D             G GFV F 
Sbjct: 9   SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 68

Query: 149 EEVVADRV-SRRSHEICGQQVAIDSATP 175
            E        R    +  + + +   T 
Sbjct: 69  NEADYKAALCRHKQYMGNRFIQVHPITK 96

>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 = 38.6 bits (89), Expect = 8e-05
 Identities = 15/93 (16%), Positives = 29/93 (31%), Gaps = 9/93 (9%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE 150
           Y  GE +    K +++  L    T  DL   F+RF       +  R          F   
Sbjct: 12  YNPGEPN----KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITF 67

Query: 151 VVADRVSR-----RSHEICGQQVAIDSATPLDD 178
              +   +       +++ G+ + I+       
Sbjct: 68  PNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 4/59 (6%)

Query: 93  RGESSQRIG-KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE 150
            G   ++IG    F G L  +   EDL   FS  G I  +   +       G + F E+
Sbjct: 2   HGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR---GAKEGIILFKEK 57

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

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]

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 9/64 (14%), Positives = 24/64 (37%), Gaps = 5/64 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR-VSRRSH 161
            + V   PQ +    +   F+++G IL   +        +  + +  ++ A + +S+   
Sbjct: 6   WVTVFGFPQASA-SYILLQFAQYGNILKHVMSN---TGNWMHIRYQSKLQARKALSKDGR 61

Query: 162 EICG 165
               
Sbjct: 62  IFGE 65

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 11/78 (14%), Positives = 24/78 (30%), Gaps = 4/78 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV--YVPKRTGH-RGFGFVTFAEEVVADR-VS 157
               +  +P   T  D+ ++        +    +    G   G   V F  E  A +   
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 158 RRSHEICGQQVAIDSATP 175
               ++ G++  +   T 
Sbjct: 69  LHRKKLNGREAFVHVVTL 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 4e-04
 Identities = 16/86 (18%), Positives = 27/86 (31%), Gaps = 6/86 (6%)

Query: 94  GESSQRIGK-KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTGH-RGFGFVTFAE 149
           G SS + G   I V  +P   + +++  +F  +  I           G   G   V F  
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 150 EVVADRV--SRRSHEICGQQVAIDSA 173
              A           I  ++V +   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 36.2 bits (83), Expect = 5e-04
 Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADR 155
           +  G L    +   L     + G +  + +P    ++ + F  +     + R
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKR 71

>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 = 35.1 bits (80), Expect = 9e-04
 Identities = 13/89 (14%), Positives = 26/89 (29%), Gaps = 12/89 (13%)

Query: 92  GRGESSQRIGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE 150
           GR E+     + + +      +     L +    FG I +             F+  A  
Sbjct: 3   GRVETR----RVVHIMDFQRGKNLRYQLLQLVEPFGVISNH---LILNKINEAFIEMATT 55

Query: 151 VVA----DRVSRRSHEICGQQVAIDSATP 175
             A    D  +     + G+ V +  +  
Sbjct: 56  EDAQAAVDYYTTTPALVFGKPVRVHLSQK 84

>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 = 35.7 bits (81), Expect = 0.001
 Identities = 18/62 (29%), Positives = 25/62 (40%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEV 151
           G   SS R    I    LP    A +++  FSRFG +  V +P+        F+   E  
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 152 VA 153
            A
Sbjct: 61  KA 62

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.001
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRTGHRGFGFVTFAEEVVADR-V 156
              + +  LP   + E++ ++FS    + +        +    G  FV FA + +A++ +
Sbjct: 15  DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL 74

Query: 157 SRRSHEICGQQVAIDSATP--LDDAGPS 182
            +    I  + + I  ++   +  +GPS
Sbjct: 75  KKHKERIGHRYIEIFKSSRAEVRTSGPS 102

>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 = 34.3 bits (78), Expect = 0.002
 Identities = 16/93 (17%), Positives = 29/93 (31%), Gaps = 2/93 (2%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFA-E 149
                    G  + +  LP  AT  D+  +FS    +         G   G   V FA  
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATH 65

Query: 150 EVVADRVSRRSHEICGQQVAIDSATPLDDAGPS 182
           E     +++    +  + V +   +    +G  
Sbjct: 66  EDAVAAMAKDKANMQHRYVELFLNSTAGTSGSG 98

>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 = 34.0 bits (77), Expect = 0.003
 Identities = 11/78 (14%), Positives = 24/78 (30%), Gaps = 4/78 (5%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVV--ADRVSRRS 160
            +++  LP     ++L      FG+++   + + +     G      E     + V    
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 161 H--EICGQQVAIDSATPL 176
           +   I           PL
Sbjct: 80  NGKFIKTPPGVSAPTEPL 97

>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 = 34.9 bits (79), Expect = 0.003
 Identities = 17/79 (21%), Positives = 28/79 (35%), Gaps = 5/79 (6%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGF---GFVTFAEEVVADRVSR 158
           + + V  +P       LR+ F R+G I  V +      R     GFV F     A +   
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 159 R--SHEICGQQVAIDSATP 175
                 I  +++ +  A  
Sbjct: 103 GLNGFNILNKRLKVALAAS 121

>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 = 34.0 bits (77), Expect = 0.003
 Identities = 17/87 (19%), Positives = 26/87 (29%), Gaps = 7/87 (8%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRV----S 157
             + V  L +     DL     +FG I  V +      +    V F     A       +
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAA 72

Query: 158 RRSHEICGQQVAIDSATPLDDAGPSQN 184
                I GQQ   + +T      P  +
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITRPGNS 99

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	234
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.94
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.85
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.85
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.82
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.8
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.8
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.79
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.79
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.79
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.79
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.78
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.78
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.78
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.76
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.76
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.76
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.71
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.67
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.53
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.52
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.49
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.47
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.4
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.31
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.3
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.28
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.28
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.26
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.26
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.26
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.26
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.26
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.25
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.25
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.25
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.23
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.22
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.19
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.19
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.18
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.17
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.17
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.16
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.14
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.14
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.13
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.12
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.11
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.1
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.1
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.09
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.09
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.08
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.07
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.06
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.05
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.04
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.02
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.01
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.0
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.98
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.98
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.97
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.97
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.95
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.93
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.92
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.91
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.91
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.9
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.9
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.89
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	98.87
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.86
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.84
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.83
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.77
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.75
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.74
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.73
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.72
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.65
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.65
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.62
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.6
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.6
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.6
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.57
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.49
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.39
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.37
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.34
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.34
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.33
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.33
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.3
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.3
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.3
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.26
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.2
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.76
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	97.52
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.45
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.13
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.0
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.02
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	90.37
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	82.78

>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=99.94  E-value=2e-26  Score=175.08  Aligned_cols=137  Identities=31%  Similarity=0.604  Sum_probs=115.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCCCCCCCccCCCCCCCCCCccchhhhhhhhcC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (234)
                      |++|+.|+.++|||||+|.+.++|++|+. ....+..+.+.+....+........                         
T Consensus        38 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------   92 (183)
T d1u1qa_          38 VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG-------------------------   92 (183)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTTGGGSTT-------------------------
T ss_pred             eeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcccccccc-------------------------
Confidence            35788999999999999999999999996 4668888988887765543322111                         


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHH
Q 026724           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRV  156 (234)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A  156 (234)
                                       .....++|||+|||+.+|+++|+++|+.||.|..+.|+  ..++ ++|||||+|.+.++|.+|
T Consensus        93 -----------------~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~A  155 (183)
T d1u1qa_          93 -----------------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  155 (183)
T ss_dssp             -----------------TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             -----------------cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHH
Confidence                             14456899999999999999999999999999999888  4556 899999999999999999


Q ss_pred             Hh-cCCccCCeEeEEEeCCCCCCC
Q 026724          157 SR-RSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       157 ~~-~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      |. +.+.|+|+.|+|.+|.|++++
T Consensus       156 l~~~~~~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         156 VIQKYHTVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             HTSSCEEETTEEEEEEECCCHHHH
T ss_pred             HHhCCCeECCEEEEEEecCCcccc
Confidence            84 667899999999999987654

>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=99.88  E-value=1.2e-22  Score=135.94  Aligned_cols=82  Identities=33%  Similarity=0.508  Sum_probs=75.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~  174 (234)
                      .....+|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++||.+.+.|+|+.|.|+++.
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCC
Confidence            3456889999999999999999999999999999998  5567 999999999999999999998889999999999999


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      +++++
T Consensus        85 ~k~~~   89 (90)
T d2cqga1          85 SKQSQ   89 (90)
T ss_dssp             TTCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.87  E-value=1.2e-21  Score=133.60  Aligned_cols=83  Identities=25%  Similarity=0.386  Sum_probs=74.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ...+++|||+|||+++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|+.||+  ++..|.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999998  4567 99999999999999999984  67799999999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      +.++.+..
T Consensus        85 a~~~~~~~   92 (99)
T d1whwa_          85 STIKKEAS   92 (99)
T ss_dssp             CCCCSTTC
T ss_pred             CCCCCccC
Confidence            99876544

>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=99.86  E-value=3.7e-22  Score=133.20  Aligned_cols=81  Identities=35%  Similarity=0.675  Sum_probs=73.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcCCccCCeEeEEEeCCCCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRSHEICGQQVAIDSATPLDD  178 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~a~~~~~  178 (234)
                      ..+++|||+|||+++|+++|+++|++||.|.+|.++..  +++||||+|.+.++|++||.+++.|+|+.|.|+++.++..
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~--~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--CCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec--cCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCCCCC
Confidence            35789999999999999999999999999999988643  6899999999999999999988999999999999998776


Q ss_pred             CCC
Q 026724          179 AGP  181 (234)
Q Consensus       179 ~~~  181 (234)
                      ...
T Consensus        81 ~~~   83 (88)
T d1wf0a_          81 SNS   83 (88)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            544

>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=99.86  E-value=1.2e-21  Score=134.27  Aligned_cols=79  Identities=35%  Similarity=0.611  Sum_probs=72.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~~  176 (234)
                      .++|||+|||+++++++|+++|++||.|..+.|+  +.++ ++|||||+|.+.++|++|| ++++.|+|+.|.|++|.|+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            4789999999999999999999999999999998  4456 9999999999999999998 4778999999999999998


Q ss_pred             CCC
Q 026724          177 DDA  179 (234)
Q Consensus       177 ~~~  179 (234)
                      +++
T Consensus       100 e~~  102 (103)
T d1x4ba1         100 EES  102 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.86  E-value=1.5e-21  Score=128.55  Aligned_cols=75  Identities=25%  Similarity=0.454  Sum_probs=69.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      +++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++||  +++..+.|+.|+|++|+|
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            4689999999999999999999999999999988  5677 9999999999999999998  478899999999999986

>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=99.86  E-value=9.3e-22  Score=131.53  Aligned_cols=81  Identities=30%  Similarity=0.514  Sum_probs=73.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...++|||+|||+++++++|+++|++||+|.+|.|+  +.++ ++|||||+|.+.++|++|+.  ++..|+|+.|+|++|
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            356799999999999999999999999999999998  5567 99999999999999999984  778999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      +|+..+
T Consensus        83 ~p~~~k   88 (89)
T d2cqba1          83 KPMRIK   88 (89)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987543

>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=99.85  E-value=3.5e-21  Score=129.70  Aligned_cols=81  Identities=21%  Similarity=0.328  Sum_probs=72.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ...+++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|..|+.  ++..|+|+.|+|+|
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            4467899999999999999999999999999999998  5566 89999999999999999984  77899999999999


Q ss_pred             CCCCCC
Q 026724          173 ATPLDD  178 (234)
Q Consensus       173 a~~~~~  178 (234)
                      +.+..+
T Consensus        84 a~~~~~   89 (93)
T d1h2vz_          84 DAGFKE   89 (93)
T ss_dssp             ESCCCT
T ss_pred             cCCCCC
Confidence            876543

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.5e-21  Score=129.71  Aligned_cols=80  Identities=25%  Similarity=0.513  Sum_probs=72.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|+.  ++..|.|+.|+|++|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            346799999999999999999999999999999998  4567 99999999999999999984  778999999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      .++..
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            98764

>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=99.85  E-value=1.1e-20  Score=136.78  Aligned_cols=82  Identities=23%  Similarity=0.436  Sum_probs=73.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|..||.  +++.|+|+.|+|++|
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345789999999999999999999999999999988  5677 99999999999999999984  778999999999999


Q ss_pred             CCCCCCC
Q 026724          174 TPLDDAG  180 (234)
Q Consensus       174 ~~~~~~~  180 (234)
                      .++..+.
T Consensus       120 ~~~~~~p  126 (139)
T d1u6fa1         120 ASGHQRP  126 (139)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            8876553

>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=99.85  E-value=4.3e-21  Score=131.48  Aligned_cols=81  Identities=27%  Similarity=0.460  Sum_probs=73.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      +++++|||+|||+++++++|+++|++||.|.++.++  +.++ ++|||||+|.+.++|+.||  +++..|.|+.|+|+++
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            456789999999999999999999999999999887  5566 8999999999999999998  4788999999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      .++.+.
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            998764

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.85  E-value=2.5e-21  Score=129.05  Aligned_cols=79  Identities=24%  Similarity=0.435  Sum_probs=71.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~  172 (234)
                      .....+|||+|||+++|+++|+++|++||.|.+|+|+  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|+|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4457899999999999999999999999999999988  4567 9999999999999999998  477899999999999


Q ss_pred             CCCC
Q 026724          173 ATPL  176 (234)
Q Consensus       173 a~~~  176 (234)
                      |.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9876

>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=99.85  E-value=1.2e-20  Score=127.10  Aligned_cols=81  Identities=32%  Similarity=0.543  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++++++|+++|++||.|.+|.++.+.+ +++||||+|.+.++|.+||  +++..|.|+.|+|++|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            45577899999999999999999999999999999995555 8999999999999999998  47889999999999999


Q ss_pred             CCCC
Q 026724          175 PLDD  178 (234)
Q Consensus       175 ~~~~  178 (234)
                      ++..
T Consensus        88 ~r~~   91 (93)
T d2cq3a1          88 ARVM   91 (93)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            8754

>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=99.85  E-value=3.4e-21  Score=128.74  Aligned_cols=79  Identities=24%  Similarity=0.389  Sum_probs=71.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..+|||+|||+++++++|+++|++||.|.++.|+.+.+ ++|||||+|.+.++|++||.  ++..|.|+.|.|++++++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            45799999999999999999999999999999995555 89999999999999999994  6679999999999999876


Q ss_pred             CC
Q 026724          178 DA  179 (234)
Q Consensus       178 ~~  179 (234)
                      ++
T Consensus        88 ~R   89 (89)
T d1cvja2          88 ER   89 (89)
T ss_dssp             TC
T ss_pred             CC
Confidence            53

>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=99.85  E-value=1.4e-21  Score=126.10  Aligned_cols=71  Identities=35%  Similarity=0.681  Sum_probs=66.0

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      +|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++||. +.+.|+|+.|+|++|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            69999999999999999999999999999998  5567 99999999999999999995 567999999999876

>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=99.85  E-value=1.3e-20  Score=129.26  Aligned_cols=81  Identities=37%  Similarity=0.607  Sum_probs=71.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHhc-CCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSRR-SHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~a  173 (234)
                      +...++|||+|||+.+++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++||.. .+.|+|+.|.|++|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a   86 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLA   86 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEES
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            4456789999999999999999999999999999998  5567 999999999999999999953 34899999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      .++..
T Consensus        87 ~~~~~   91 (103)
T d2cqda1          87 YLGAK   91 (103)
T ss_dssp             TTTCC
T ss_pred             CCCCC
Confidence            86543

>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=99.85  E-value=6.6e-22  Score=128.44  Aligned_cols=72  Identities=38%  Similarity=0.648  Sum_probs=67.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      ++|||+|||+++|+++|+++|++||.|.++.|+  +.++ ++|||||+|.+.++|++|| ++++.|+|+.|+|++|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            589999999999999999999999999999998  5567 9999999999999999998 5788999999999987

>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=99.85  E-value=3e-21  Score=129.26  Aligned_cols=80  Identities=26%  Similarity=0.427  Sum_probs=72.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ....++|||+|||.++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|.+||+  ++..|.|+.|+|+|
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            3456789999999999999999999999999999988  4567 99999999999999999984  67799999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      |+|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            99875

>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=99.85  E-value=5e-21  Score=126.01  Aligned_cols=75  Identities=27%  Similarity=0.475  Sum_probs=69.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      .++|||+|||+++++++|+++|++||.|.+|+|+  ..++ ++|||||+|.+.++|++|+  ++++.|.|+.|+|++|+|
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            3579999999999999999999999999999998  4455 8999999999999999998  478899999999999987

>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=99.84  E-value=4e-21  Score=126.88  Aligned_cols=75  Identities=37%  Similarity=0.563  Sum_probs=69.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      ..++|||+|||+++|+++|+++|++||.|..|.|+  +.++ ++|||||+|.+.++|++|| ++++.|+|+.|+|+.|.
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 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            45789999999999999999999999999999988  5567 9999999999999999999 47789999999999886

>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=99.84  E-value=1.1e-20  Score=126.42  Aligned_cols=82  Identities=21%  Similarity=0.299  Sum_probs=73.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||.++|+++|+++|++||.|..|.|+.+.. .++||||+|.+.++|..|+  +++..|.|+.|+|.||.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34567999999999999999999999999999999985544 7899999999999999998  47889999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++..+
T Consensus        85 ~~~~~   89 (90)
T d2cqia1          85 TPSSQ   89 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            76543

>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=99.84  E-value=4.6e-21  Score=128.43  Aligned_cols=80  Identities=34%  Similarity=0.542  Sum_probs=72.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ...+|||+|||+++++++|+++|++||.|..+.++  +.++ ++|||||+|.++++|+.|+  ++++.|.|+.|+|++|.
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            46789999999999999999999999999999877  5566 9999999999999999998  47889999999999998


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++.+.
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.84  E-value=9.2e-21  Score=127.84  Aligned_cols=81  Identities=32%  Similarity=0.588  Sum_probs=72.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee---cCCC-CcceEEEEEcChHHHHHHHh---cCCccCCeEeEE
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTG-HRGFGFVTFAEEVVADRVSR---RSHEICGQQVAI  170 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~---~~~~-~~g~afV~f~~~~~a~~A~~---~~~~~~g~~i~v  170 (234)
                      ...+.+|||+|||+++++++|+++|++||.|.+|.|+   ..++ ++|||||+|.+.++|.+||.   ++..|+|++|.|
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            3457889999999999999999999999999999997   2366 89999999999999999984   567899999999


Q ss_pred             EeCCCCCC
Q 026724          171 DSATPLDD  178 (234)
Q Consensus       171 ~~a~~~~~  178 (234)
                      +||.++..
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99988764

>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=99.84  E-value=4.7e-21  Score=123.82  Aligned_cols=71  Identities=39%  Similarity=0.754  Sum_probs=65.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      +|||+|||+++|+++|+++|++||+|..|.|+  +.++ ++|||||+|.+.++|++||. +.+.|+|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999998  5667 99999999999999999984 677999999999764

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.3e-21  Score=125.92  Aligned_cols=77  Identities=18%  Similarity=0.446  Sum_probs=70.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~  176 (234)
                      .+|||+|||+++|+++|+++|++||+|.+|+|+  +.++ ++|||||+|.++++|..|+.  ++..|.|+.|.|++|.+.
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            479999999999999999999999999999998  5667 99999999999999999995  677999999999999876


Q ss_pred             CC
Q 026724          177 DD  178 (234)
Q Consensus       177 ~~  178 (234)
                      ..
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.83  E-value=3.6e-20  Score=127.34  Aligned_cols=83  Identities=20%  Similarity=0.409  Sum_probs=71.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee---cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~---~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~  172 (234)
                      ..+.++|||+|||+++|+++|+++|++|| |.++.++   ..++ ++|||||+|.+.++|++|+ ++++.|+|+.|+|++
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999 6677666   3355 8999999999999998877 578899999999999


Q ss_pred             CCCCCCCCC
Q 026724          173 ATPLDDAGP  181 (234)
Q Consensus       173 a~~~~~~~~  181 (234)
                      |.++.....
T Consensus        91 a~~~~~~~~   99 (104)
T d1wi8a_          91 ADQAQDKDS   99 (104)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCCCCCCC
Confidence            998776543

>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=99.83  E-value=1.5e-20  Score=122.74  Aligned_cols=73  Identities=33%  Similarity=0.688  Sum_probs=67.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      .++|||+|||+++|+++|+++|++||.|..+.++  +.++ ++|||||+|.+.++|++|+ ++++.|+|+.|+|+.|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            5799999999999999999999999999999888  4566 8999999999999999998 5788999999999987

>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=99.83  E-value=1.6e-20  Score=122.84  Aligned_cols=72  Identities=29%  Similarity=0.376  Sum_probs=67.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      .|||+|||+++|+++|+++|++||+|.+|+|+  +.++ ++|||||+|.++++|..|+.  ++..+.|++|+|.||+
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            69999999999999999999999999999999  5566 89999999999999999994  6779999999999985

>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=99.83  E-value=3.7e-20  Score=125.12  Aligned_cols=79  Identities=24%  Similarity=0.449  Sum_probs=70.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ....++|||+|||+++|+++|+++|++||.|..+.+.....+++||||+|.+.++|+.||  ++++.|.|++|+|+||++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            456779999999999999999999999999999988744448899999999999999998  478899999999999976


Q ss_pred             C
Q 026724          176 L  176 (234)
Q Consensus       176 ~  176 (234)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.83  E-value=1.3e-20  Score=125.07  Aligned_cols=78  Identities=22%  Similarity=0.391  Sum_probs=67.7

Q ss_pred             CCCEEEEeCCCCCCC-HHHHHHHHhhcCceeEEEee---cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeC
Q 026724          100 IGKKIFVGRLPQEAT-AEDLRRYFSRFGRILDVYVP---KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSA  173 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~-~~~l~~~f~~~G~v~~~~~~---~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a  173 (234)
                      ..++|||+|||++++ +++|+++|++||.|.+|.|+   +.++ ++|||||+|.+.++|++|++ +++.|.|+.|+|++|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            467999999999976 56799999999999999987   2455 89999999999999999994 788999999999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      .+++
T Consensus        83 ~~kP   86 (86)
T d2ghpa3          83 DKKP   86 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9764

>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=99.83  E-value=2.4e-20  Score=121.42  Aligned_cols=72  Identities=24%  Similarity=0.377  Sum_probs=67.0

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      +|||+|||+++++++|+++|++||.|.+|.|+ ..++ ++|||||+|.+.++|.+|+.  ++..+.|++|+|+++.
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            69999999999999999999999999999998 4456 99999999999999999984  7889999999999986

>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=99.82  E-value=1.6e-20  Score=123.86  Aligned_cols=76  Identities=29%  Similarity=0.505  Sum_probs=68.0

Q ss_pred             EEEeCCCCCCCHHHHHHHHhhcCceeEE-Eee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCCC
Q 026724          104 IFVGRLPQEATAEDLRRYFSRFGRILDV-YVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       104 l~v~nl~~~~~~~~l~~~f~~~G~v~~~-~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~~  177 (234)
                      |||+|||+++|+++|+++|++||.|..+ .|+  +.++ ++|||||+|.+.++|.+||.  ++..++|++|+|++|.++.
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            7999999999999999999999998664 555  4566 89999999999999999984  6789999999999999876


Q ss_pred             CC
Q 026724          178 DA  179 (234)
Q Consensus       178 ~~  179 (234)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.82  E-value=1.6e-20  Score=123.20  Aligned_cols=74  Identities=14%  Similarity=0.216  Sum_probs=64.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      ++|||+|||+++|+++|+++|++||.|..+.++  ..++ ++|||||+|.+.++|.+|+  +++..+.|++|.|++++|
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            689999999999999999999999999877766  4456 9999999999999999998  478899999999999987

>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=99.82  E-value=5.7e-20  Score=124.97  Aligned_cols=82  Identities=26%  Similarity=0.409  Sum_probs=71.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--c------CCccCCe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--R------SHEICGQ  166 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~------~~~~~g~  166 (234)
                      ....++|||+|||+++|+++|+++|++||.|.++.++  +.++ ++|||||+|.+.++|.+||.  +      +..|+|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456789999999999999999999999999999888  4455 89999999999999999984  2      3478999


Q ss_pred             EeEEEeCCCCCCC
Q 026724          167 QVAIDSATPLDDA  179 (234)
Q Consensus       167 ~i~v~~a~~~~~~  179 (234)
                      .|+|.+|.++.+.
T Consensus        85 ~l~v~~a~~k~~a   97 (98)
T d1x4ha1          85 QLKVDLAVTRDEA   97 (98)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCCcC
Confidence            9999999987653

>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=99.82  E-value=3.4e-21  Score=129.12  Aligned_cols=79  Identities=20%  Similarity=0.352  Sum_probs=71.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      .....+|||+|||+++|+++|+++|++||.|..+.|+ +.++ ++|||||+|.+.++|++|| ++++.|.|+.|+|.+|+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            4456799999999999999999999999999888877 4456 9999999999999999999 47889999999999998


Q ss_pred             CC
Q 026724          175 PL  176 (234)
Q Consensus       175 ~~  176 (234)
                      ++
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.82  E-value=2.8e-20  Score=123.07  Aligned_cols=75  Identities=27%  Similarity=0.559  Sum_probs=67.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCC--eEeEEE
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICG--QQVAID  171 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g--~~i~v~  171 (234)
                      ...++|||+|||+++|+++|+++|++||+|.+|+|+  +.++ ++|||||+|.+.++|++|+  +++..+.|  ++|.|+
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            346789999999999999999999999999999998  4566 9999999999999999998  47788887  569999


Q ss_pred             eC
Q 026724          172 SA  173 (234)
Q Consensus       172 ~a  173 (234)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.81  E-value=5.3e-20  Score=121.77  Aligned_cols=75  Identities=25%  Similarity=0.425  Sum_probs=67.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCC--eEeEEE
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICG--QQVAID  171 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g--~~i~v~  171 (234)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+  +.++ ++|||||+|.+.++|.+|+.  ++..+.|  ++|+|+
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            356789999999999999999999999999999988  4567 99999999999999999994  6667766  889999


Q ss_pred             eC
Q 026724          172 SA  173 (234)
Q Consensus       172 ~a  173 (234)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            87

>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=99.81  E-value=5.2e-20  Score=121.86  Aligned_cols=74  Identities=24%  Similarity=0.479  Sum_probs=66.0

Q ss_pred             EEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC----CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG----HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus       104 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~----~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      |||+|||+++|+++|+++|++||.|.+|.|+  +.++    ++|||||+|.+.++|.+|+.  +++.|+|+.|.|+++.+
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            8999999999999999999999999999988  3332    58999999999999999984  77899999999999975


Q ss_pred             CC
Q 026724          176 LD  177 (234)
Q Consensus       176 ~~  177 (234)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.81  E-value=7.6e-20  Score=124.10  Aligned_cols=78  Identities=27%  Similarity=0.508  Sum_probs=68.1

Q ss_pred             CCCCCEEEEeCCC-CCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~-~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+||| ..+++++|+++|++||.|.+|.|     +++||||+|++.++|++||  +++..|.|+.|+|+++.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-----ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-----eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4456789999997 57889999999999999999999     4799999999999999998  47789999999999998


Q ss_pred             CCCCCC
Q 026724          175 PLDDAG  180 (234)
Q Consensus       175 ~~~~~~  180 (234)
                      ++....
T Consensus        87 ~~~~~~   92 (98)
T d1wf2a_          87 EPKVNR   92 (98)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            755443

>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=99.81  E-value=2.5e-20  Score=120.45  Aligned_cols=71  Identities=45%  Similarity=0.763  Sum_probs=65.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus       103 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      +|||+|||+++|+++|+++|++||.|..+.++  +.++ +++||||+|.+.++|++|+ ++++.|+|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999887  5566 9999999999999999998 4788999999999986

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.9e-20  Score=127.80  Aligned_cols=76  Identities=18%  Similarity=0.400  Sum_probs=69.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~~~  176 (234)
                      .++|||+|||+++++++|+++|++||.|.+|+|+  +.++ ++|||||+|.+.++|.+|+ +++..|.|+.|.|+++.++
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~~~   97 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCCC
Confidence            4689999999999999999999999999999998  4567 9999999999999999998 5788999999999998654

>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=99.81  E-value=6e-20  Score=120.99  Aligned_cols=72  Identities=29%  Similarity=0.406  Sum_probs=65.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEE
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAI  170 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v  170 (234)
                      .+.++|||+|||+++|+++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|+  +++..|+|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            346789999999999999999999999999999988  4566 8999999999999999998  4778999999987

>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=99.81  E-value=1.3e-19  Score=122.57  Aligned_cols=76  Identities=24%  Similarity=0.379  Sum_probs=69.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..++|||+|||.++++++|+++|++||.|.+|+|+++   +|||||+|.+.++|.+|+  +++..|.|+.|+|.|++++.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~---kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec---ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4678999999999999999999999999999999875   799999999999999998  47889999999999998764


Q ss_pred             C
Q 026724          178 D  178 (234)
Q Consensus       178 ~  178 (234)
                      .
T Consensus        94 ~   94 (96)
T d1x4ga1          94 D   94 (96)
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=99.81  E-value=4e-20  Score=127.09  Aligned_cols=78  Identities=29%  Similarity=0.601  Sum_probs=71.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      .++|||+|||+++++++|+++|++||.|.+|.|+  +.++ ++|||||+|.+.++|++|+.  +++.|.|+.|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999988  5677 99999999999999999984  67799999999999987


Q ss_pred             CCC
Q 026724          176 LDD  178 (234)
Q Consensus       176 ~~~  178 (234)
                      +..
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            653

>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=99.80  E-value=1.3e-19  Score=126.67  Aligned_cols=78  Identities=18%  Similarity=0.406  Sum_probs=70.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      ..+++|||+|||+++++++|+++|++||.|.+|++..+..++|||||+|.+.++|..||  ++++.|.|+.|.|.++.+.
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            35689999999999999999999999999999998854338999999999999999998  4788999999999998754

>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=99.80  E-value=3.2e-19  Score=122.47  Aligned_cols=84  Identities=17%  Similarity=0.245  Sum_probs=72.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      .....+|||+|||+++|+++|+++|+++|.|..+.++  +.++ ++|||||+|.+.++|++|+ ++.+.|.||.|+|.++
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            4456689999999999999999999999998775444  5555 9999999999999999998 4778999999999999


Q ss_pred             CCCCCCCC
Q 026724          174 TPLDDAGP  181 (234)
Q Consensus       174 ~~~~~~~~  181 (234)
                      .+++...+
T Consensus        92 ~~~~~~~s   99 (104)
T d1wg5a_          92 SRAEVRTS   99 (104)
T ss_dssp             CTTTSCCS
T ss_pred             CHHHhccC
Confidence            88765543

>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=99.80  E-value=2e-19  Score=122.91  Aligned_cols=83  Identities=19%  Similarity=0.314  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE--------EEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~  164 (234)
                      ....++|||+|||+++|+++|+++|++||.|..        +.+.  +.++ +++||||+|.++++|.+||+  ++..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            456789999999999999999999999998753        3333  3456 88999999999999999984  788999


Q ss_pred             CeEeEEEeCCCCCCCC
Q 026724          165 GQQVAIDSATPLDDAG  180 (234)
Q Consensus       165 g~~i~v~~a~~~~~~~  180 (234)
                      |+.|+|++|+++.++.
T Consensus        85 gr~i~V~~a~~~~p~~  100 (101)
T d2cpea1          85 GSKLKVSLARKKPPMN  100 (101)
T ss_dssp             TEECEEECSSCCCCST
T ss_pred             CEEEEEEEcCCCCCCC
Confidence            9999999999877653

>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=99.80  E-value=1.8e-19  Score=119.36  Aligned_cols=75  Identities=27%  Similarity=0.601  Sum_probs=68.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..++|||+|||.++++++|+++|++||.|.+|.+.++   ++||||+|.+.++|.+|+.  ++..|.|+.|+|+||.+..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~---k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT---TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc---cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            4578999999999999999999999999999999864   7999999999999999984  7889999999999998764

>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=99.80  E-value=1.6e-19  Score=119.32  Aligned_cols=75  Identities=16%  Similarity=0.325  Sum_probs=68.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSAT  174 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~  174 (234)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+ ..++ ++|||||+|.+.++|++||. ++..+.|+.|.|.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            35789999999999999999999999999999998 4566 89999999999999999994 6789999999999864

>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=99.80  E-value=1.8e-19  Score=121.90  Aligned_cols=79  Identities=28%  Similarity=0.501  Sum_probs=68.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCc-eeEEEeec---CCC-CcceEEEEEcChHHHHHHHhc----CCccCCeEeEEEe
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPK---RTG-HRGFGFVTFAEEVVADRVSRR----SHEICGQQVAIDS  172 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~~---~~~-~~g~afV~f~~~~~a~~A~~~----~~~~~g~~i~v~~  172 (234)
                      ++|||+|||.++++++|+++|++||. |..+.+++   .++ ++|||||+|.++++|..|+..    ...+.|+.|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 88998873   345 899999999999999999843    3366899999999


Q ss_pred             CCCCCCCC
Q 026724          173 ATPLDDAG  180 (234)
Q Consensus       173 a~~~~~~~  180 (234)
                      |+|+.+..
T Consensus        82 A~p~~~~~   89 (96)
T d2disa1          82 AEPEIDVD   89 (96)
T ss_dssp             SCSSCSTT
T ss_pred             cCCCCCCC
Confidence            99877553

>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=99.80  E-value=2.1e-19  Score=115.81  Aligned_cols=72  Identities=18%  Similarity=0.291  Sum_probs=65.6

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      ++|||+|||+++++++|+++|++||.|..|+++.+.. .++||||+|.+.++|.+|| ++++.|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999985444 7789999999999999998 5778999999999875

>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=99.79  E-value=5.2e-19  Score=117.18  Aligned_cols=77  Identities=21%  Similarity=0.259  Sum_probs=69.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      ...++|||+|||+++++++|+++|++||.|..+.+.+   +++||||+|.+.++|..|+  +++..|.|+.|.|.||+|+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~---~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc---ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            3467899999999999999999999999988777754   5899999999999999998  4777999999999999987


Q ss_pred             CC
Q 026724          177 DD  178 (234)
Q Consensus       177 ~~  178 (234)
                      ..
T Consensus        83 ~~   84 (86)
T d2cpda1          83 DK   84 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.79  E-value=2.9e-19  Score=122.22  Aligned_cols=82  Identities=21%  Similarity=0.265  Sum_probs=70.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a~  174 (234)
                      .....+|||+|||+++|+++|+++|+.|+.+ .|.++ ..++ ++|||||+|.+.++|++|+ ++.+.|.||.|+|.++.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            4567899999999999999999999999854 56555 5556 8999999999999999998 47889999999999998


Q ss_pred             CCCCCC
Q 026724          175 PLDDAG  180 (234)
Q Consensus       175 ~~~~~~  180 (234)
                      ++....
T Consensus        91 ~~~~~~   96 (102)
T d1weza_          91 TAGTSG   96 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776544

>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=99.79  E-value=5.3e-19  Score=116.32  Aligned_cols=75  Identities=21%  Similarity=0.348  Sum_probs=66.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCcc-CCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEI-CGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~-~g~~i~v~~a~  174 (234)
                      .+++++|||+|||.++++++|+++|++||.|..|+++++  .++||||+|.+.++|..|+.  ++..| .|+.|+|+||+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN--RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT--TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc--cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            456789999999999999999999999999999999854  57999999999999999984  66666 57899999986

>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=99.79  E-value=1e-19  Score=118.95  Aligned_cols=75  Identities=25%  Similarity=0.398  Sum_probs=66.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCC-ccCCeEeEEEeCCCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSH-EICGQQVAIDSATPLDD  178 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~-~~~g~~i~v~~a~~~~~  178 (234)
                      ++|||+|||+++|+++|+++|++||.|..+.+..   ++|||||+|.+.++|.+|+.  ++. .++|++|+|++|.|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~---~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec---ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            4799999999999999999999999987766664   37999999999999999984  564 69999999999999876


Q ss_pred             C
Q 026724          179 A  179 (234)
Q Consensus       179 ~  179 (234)
                      +
T Consensus        79 r   79 (80)
T d2cqha1          79 R   79 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=8.5e-20  Score=125.03  Aligned_cols=82  Identities=22%  Similarity=0.333  Sum_probs=73.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~  172 (234)
                      ..++++|||+|||.++++++|+++|++||.|..+.++  ..++ +++||||+|.+.++|..||.  ++..|.|+.|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3457899999999999999999999999999888777  4456 99999999999999999984  67899999999999


Q ss_pred             CCCCCCC
Q 026724          173 ATPLDDA  179 (234)
Q Consensus       173 a~~~~~~  179 (234)
                      |+++.++
T Consensus        95 ak~k~~r  101 (102)
T d2cpxa1          95 GKNKKQR  101 (102)
T ss_dssp             CCCCSCC
T ss_pred             CCCcccC
Confidence            9988764

>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=99.78  E-value=4.3e-19  Score=120.33  Aligned_cols=80  Identities=15%  Similarity=0.227  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATP  175 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~  175 (234)
                      .....+|||+|||+++++++|+++|++||.|+.|.|..    +|||||+|.+.++|++||  +++..|.|+.|+|.++++
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            45678999999999999999999999999999999874    589999999999999998  477899999999999987


Q ss_pred             CCCCCC
Q 026724          176 LDDAGP  181 (234)
Q Consensus       176 ~~~~~~  181 (234)
                      +.++..
T Consensus        88 ~~~~~~   93 (98)
T d1wg4a_          88 YPERSS   93 (98)
T ss_dssp             ECCCSS
T ss_pred             CCCCCC
Confidence            765543

>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=99.78  E-value=4e-19  Score=121.31  Aligned_cols=78  Identities=17%  Similarity=0.356  Sum_probs=69.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      ....++|||+|||+++++++|+++|++||.|..+.+. ..++ ++|||||+|.+.++|.+|+  +++..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            3446799999999999999999999999999999888 4455 8999999999999999998  5888999999988877


Q ss_pred             CC
Q 026724          174 TP  175 (234)
Q Consensus       174 ~~  175 (234)
                      +|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            66

>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=99.78  E-value=5.7e-19  Score=115.02  Aligned_cols=74  Identities=27%  Similarity=0.371  Sum_probs=66.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      ..+++|||+||+  +|+++|+++|++||.|.+|.+.+.   ++||||+|.+.++|.+|+  +++..|+|+.|+|.|++++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~---~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP---RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT---TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC---CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            357899999996  899999999999999999999864   789999999999999998  4788999999999999876


Q ss_pred             C
Q 026724          177 D  177 (234)
Q Consensus       177 ~  177 (234)
                      +
T Consensus        78 P   78 (79)
T d2bz2a1          78 P   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=1e-19  Score=120.89  Aligned_cols=74  Identities=16%  Similarity=0.192  Sum_probs=66.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLDDA  179 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~~~  179 (234)
                      ++|||+|||+++++++|+++|++||.|.++.+.+    .|||||+|.+.++|++||  +++..|.|+.|+|.++.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~~   76 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   76 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc----cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcCC
Confidence            4799999999999999999999999999999875    389999999999999998  4788999999999988766543

>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=99.77  E-value=1.4e-18  Score=115.52  Aligned_cols=77  Identities=13%  Similarity=0.248  Sum_probs=66.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCcc-CCeEeEEEeCCC
Q 026724           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEI-CGQQVAIDSATP  175 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~-~g~~i~v~~a~~  175 (234)
                      +++++|||+|||+++++++|+++|++||.|..+.+... ..++||||+|++.++|.+|+  +++..| +|+.|+|+|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS-SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee-cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            45789999999999999999999999999988766521 15789999999999999998  456666 689999999986


Q ss_pred             C
Q 026724          176 L  176 (234)
Q Consensus       176 ~  176 (234)
                      .
T Consensus        87 ~   87 (88)
T d2adca2          87 T   87 (88)
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=99.77  E-value=5e-19  Score=118.49  Aligned_cols=79  Identities=29%  Similarity=0.505  Sum_probs=68.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHH----HHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724          100 IGKKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~----~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ++++|||+|||+++++++|++    +|++||+|.+|.+.+...++|||||+|.+.++|.+|+.  ++..+.|+.|+|.||
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            468999999999999999864    68999999999887422278999999999999999984  678999999999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      +++.+
T Consensus        82 k~~~~   86 (91)
T d1nu4a_          82 KTDSD   86 (91)
T ss_dssp             SSCCT
T ss_pred             CCCch
Confidence            87653

>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=99.77  E-value=2.2e-18  Score=119.31  Aligned_cols=75  Identities=17%  Similarity=0.273  Sum_probs=67.4

Q ss_pred             CCEEEEeCCCC-CCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCCCCC
Q 026724          101 GKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       101 ~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~~~~  177 (234)
                      +++|||+||++ .+|+++|+++|++||.|..|.|+++  .+|||||+|++.++|.+|++  ++..|.|+.|+|++++...
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~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT--TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec--ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57899999965 5999999999999999999999865  47999999999999999984  7889999999999997654

>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=99.76  E-value=4.4e-18  Score=115.16  Aligned_cols=77  Identities=22%  Similarity=0.376  Sum_probs=68.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCC--eEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICG--QQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g--~~i~v~~a  173 (234)
                      ..++++|||+|||+++++++|+++|++||.|..|.+.++   ++||||+|.+.++|+.|+.  ++..|.|  ++|+|+||
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~---~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc---ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            446789999999999999999999999999999998764   7899999999999999984  6777876  58999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      ++.+
T Consensus        91 k~~~   94 (97)
T d1whya_          91 KSGP   94 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.76  E-value=1.4e-18  Score=115.46  Aligned_cols=76  Identities=16%  Similarity=0.254  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      .+.+|||+|||++++++||+++|++|| +..+.+..   +++||||+|.+.++|++|+  +++..|.|+.|+|++++++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~---~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR---NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG---GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec---cCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            357899999999999999999999999 33333332   5899999999999999998  47889999999999997665


Q ss_pred             CC
Q 026724          178 DA  179 (234)
Q Consensus       178 ~~  179 (234)
                      ..
T Consensus        80 ~~   81 (88)
T d1wg1a_          80 LL   81 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.76  E-value=7.7e-19  Score=122.01  Aligned_cols=75  Identities=21%  Similarity=0.232  Sum_probs=68.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCCC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPLD  177 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~~  177 (234)
                      ..++|||+|||+++++++|+++|++||.|..|.|.+   +++||||+|.+.++|.+|+  +++..|.|+.|.|+|+....
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~---~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec---cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            457899999999999999999999999999998865   4799999999999999998  47889999999999986554

>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=99.76  E-value=6.7e-19  Score=119.05  Aligned_cols=79  Identities=20%  Similarity=0.318  Sum_probs=69.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeCC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSAT  174 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a~  174 (234)
                      ....++|||+|||+++|+++|+++|++||.|..+..   ++ +++||||+|.+.++|++|+.  ++..|+|+.|+|.|+.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~---~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ---DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE---TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee---cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            345689999999999999999999999998866643   44 79999999999999999984  6779999999999999


Q ss_pred             CCCCC
Q 026724          175 PLDDA  179 (234)
Q Consensus       175 ~~~~~  179 (234)
                      ++...
T Consensus        90 ~k~~~   94 (96)
T d1fjca_          90 EKGGT   94 (96)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            88654

>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=99.76  E-value=1.3e-17  Score=114.20  Aligned_cols=79  Identities=20%  Similarity=0.189  Sum_probs=70.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh----cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR----RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~----~~~~~~g~~i~v~~a  173 (234)
                      ..++++|||+|||+++|+++|.++|++||.|..|.+.+.   +++|||+|++.++|++|+.    +...+.|++|+|.|+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~---k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF---KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec---ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            456889999999999999999999999999999999864   7999999999999999984    345789999999999


Q ss_pred             CCCCCC
Q 026724          174 TPLDDA  179 (234)
Q Consensus       174 ~~~~~~  179 (234)
                      +.++..
T Consensus        89 ~~~~~~   94 (104)
T d1wexa_          89 TSKRIT   94 (104)
T ss_dssp             SSSSCC
T ss_pred             CCCccC
Confidence            876544

>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=99.75  E-value=5e-18  Score=112.84  Aligned_cols=77  Identities=17%  Similarity=0.270  Sum_probs=69.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh----cCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR----RSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~----~~~~~~g~~i~v~~a  173 (234)
                      ..++++|||+|||+++++++|+++|++||.|.++.+.+.   +++|||+|.+.++|++|+.    +...+.|++|+|.|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~---~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~s   81 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   81 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc---ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEEC
Confidence            457899999999999999999999999999999998864   6899999999999999974    355899999999999


Q ss_pred             CCCC
Q 026724          174 TPLD  177 (234)
Q Consensus       174 ~~~~  177 (234)
                      +.++
T Consensus        82 k~~~   85 (88)
T d2cq1a1          82 NHKE   85 (88)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8664

>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=99.73  E-value=2.4e-18  Score=113.92  Aligned_cols=74  Identities=18%  Similarity=0.231  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEee-cCCC-CcceEEEEEcChHHHHHHHh--cCCccCCeEeEEEeC
Q 026724          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVP-KRTG-HRGFGFVTFAEEVVADRVSR--RSHEICGQQVAIDSA  173 (234)
Q Consensus       100 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~-~~~~-~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~a  173 (234)
                      ...+|||+|||++++++||+++|+.||.|.. +.+. ..++ ++|+|||+|.+.++|.+|++  +++.|.|++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4567999999999999999999999999865 3444 5566 89999999999999999984  778999999999875

>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=99.73  E-value=4.1e-18  Score=116.66  Aligned_cols=79  Identities=16%  Similarity=0.180  Sum_probs=68.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeE-EEee-cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVP-KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~-~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      .....+|||+|||+++|+++|+++|+.||.|.. +.+. ..++ ++|||||+|.+.++|++|| ++++.|+|+.|.|.++
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEEC
Confidence            344678999999999999999999999999876 4444 5666 9999999999999999998 4778999999999987


Q ss_pred             CCC
Q 026724          174 TPL  176 (234)
Q Consensus       174 ~~~  176 (234)
                      .++
T Consensus        85 ~~~   87 (103)
T d2cpya1          85 TLE   87 (103)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            543

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1e-17  Score=115.59  Aligned_cols=80  Identities=21%  Similarity=0.257  Sum_probs=68.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCcc--CCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEI--CGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~--~g~~i~v~~a  173 (234)
                      ..+..+|||+|||+++|+++|+++|++||.|..|.|+... ++|||||+|.+.++|+.|+  +++..|  .+++|+|.++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~-~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET-TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC-CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            3456789999999999999999999999999999888321 5899999999999999998  466666  5789999999


Q ss_pred             CCCCC
Q 026724          174 TPLDD  178 (234)
Q Consensus       174 ~~~~~  178 (234)
                      +++..
T Consensus        83 ~~~~~   87 (108)
T d2adba1          83 KLTSL   87 (108)
T ss_dssp             SSCSC
T ss_pred             CCccc
Confidence            87654

>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=99.72  E-value=2.5e-18  Score=109.93  Aligned_cols=66  Identities=23%  Similarity=0.456  Sum_probs=59.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeE
Q 026724          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVA  169 (234)
Q Consensus       104 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~  169 (234)
                      |||+|||+++|+++|+++|++||.|..+.+.  +.++ ++|||||+|.+.++|++|+  +++..|.|+.|+
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            7999999999999999999999999999887  4556 9999999999999999998  477788888764

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=4.7e-18  Score=113.10  Aligned_cols=73  Identities=21%  Similarity=0.309  Sum_probs=63.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHH---HHHHhhcCceeEEEeec--CCC----CcceEEEEEcChHHHHHHH--hcCCccCCeE
Q 026724           99 RIGKKIFVGRLPQEATAEDL---RRYFSRFGRILDVYVPK--RTG----HRGFGFVTFAEEVVADRVS--RRSHEICGQQ  167 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~~~l---~~~f~~~G~v~~~~~~~--~~~----~~g~afV~f~~~~~a~~A~--~~~~~~~g~~  167 (234)
                      ...++|||+|||+++++++|   +++|++||.|..|.|++  .++    .++||||+|.+.++|.+|+  +++..+.|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34678999999999999999   77899999999999982  222    4589999999999999998  4788999999


Q ss_pred             eEEE
Q 026724          168 VAID  171 (234)
Q Consensus       168 i~v~  171 (234)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=1.4e-17  Score=112.99  Aligned_cols=77  Identities=16%  Similarity=0.291  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh----cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR----RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~----~~~~~~g~~i~v~~  172 (234)
                      ...+++|||+|||.+ +|+++|.++|++||.|.+|.++++   +++|||+|.+.++|.+|+.    +...+.|+.|+|.+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~---k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~   91 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM---KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   91 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT---TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec---CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEE
Confidence            446789999999985 899999999999999999999864   7999999999999999983    45589999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      ++.+.
T Consensus        92 s~~~~   96 (99)
T d1x4fa1          92 SEKYK   96 (99)
T ss_dssp             ECSCS
T ss_pred             cCCcc
Confidence            97654

>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=99.71  E-value=3.4e-17  Score=105.29  Aligned_cols=69  Identities=17%  Similarity=0.323  Sum_probs=60.9

Q ss_pred             EEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeCCCC
Q 026724          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSATPL  176 (234)
Q Consensus       104 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a~~~  176 (234)
                      |||+|||+++++++|+++|++|| +..+.+.+   +++||||+|.+.++|++|+  +++..+.|++|.|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~---~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK---YKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc---cceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 55555543   5899999999999999998  4777999999999999654

>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=99.71  E-value=6.7e-18  Score=117.26  Aligned_cols=79  Identities=20%  Similarity=0.321  Sum_probs=68.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEeC
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDSA  173 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~a  173 (234)
                      .....+|||+|||+++|+++|+++|+.||.|..+.++  ..++ ++|||||+|.+.++|++|+ ++++.|+|+.|.|..+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            4457799999999999999999999999998664333  5667 9999999999999999998 5788999999999987


Q ss_pred             CCC
Q 026724          174 TPL  176 (234)
Q Consensus       174 ~~~  176 (234)
                      .++
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            543

>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=99.69  E-value=4.5e-17  Score=108.21  Aligned_cols=77  Identities=12%  Similarity=0.162  Sum_probs=67.7

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh----cCCccCCeEeEEEe
Q 026724           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR----RSHEICGQQVAIDS  172 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~----~~~~~~g~~i~v~~  172 (234)
                      ...+++|||+|||.. +|++||.++|++||.|.+|.++++   +++|||+|++.++|..|+.    +...+.|++|+|.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~---k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~   81 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   81 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc---ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEE
Confidence            456889999999986 789999999999999999999864   6899999999999999984    34579999999999


Q ss_pred             CCCCC
Q 026724          173 ATPLD  177 (234)
Q Consensus       173 a~~~~  177 (234)
                      +++..
T Consensus        82 s~~~~   86 (89)
T d1x4da1          82 SQKYK   86 (89)
T ss_dssp             ECCCT
T ss_pred             CCCcc
Confidence            97543

>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=1.4e-18  Score=116.02  Aligned_cols=73  Identities=18%  Similarity=0.319  Sum_probs=62.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-------cCCC-CcceEEEEEcChHHHHHHH-hcCCccCCeEeEEEe
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-------KRTG-HRGFGFVTFAEEVVADRVS-RRSHEICGQQVAIDS  172 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-------~~~~-~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~  172 (234)
                      ++|||+|||+++|+++|+++|++||.|..+.+.       ..++ ++|||||+|.+.++|++|+ +++..+.|+.|+|+.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            689999999999999999999999988665543       2344 8999999999999999998 578899999999975


Q ss_pred             CC
Q 026724          173 AT  174 (234)
Q Consensus       173 a~  174 (234)
                      ++
T Consensus        82 ~k   83 (90)
T d1u2fa_          82 PH   83 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.67  E-value=1.4e-16  Score=108.75  Aligned_cols=79  Identities=10%  Similarity=0.086  Sum_probs=68.1

Q ss_pred             CCCCEEEEeCCCCCC-C----HHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCccCCeEeEEE
Q 026724           99 RIGKKIFVGRLPQEA-T----AEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEICGQQVAID  171 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~-~----~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~  171 (234)
                      ..+++|||+||+.++ +    +++|+++|++||.|.++.+.+   ++++|||+|.+.++|.+|+.  ++..|.|+.|+|.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k---~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   79 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET---TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec---CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEe
Confidence            357899999999876 3    357999999999999999986   47899999999999999994  6779999999999


Q ss_pred             eCCCCCCCC
Q 026724          172 SATPLDDAG  180 (234)
Q Consensus       172 ~a~~~~~~~  180 (234)
                      |++++....
T Consensus        80 ~a~~~~~~~   88 (104)
T d1weya_          80 FAQTLHIGS   88 (104)
T ss_dssp             CCCCSSCCS
T ss_pred             ecccCCCCC
Confidence            998776543

>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=99.53  E-value=6.9e-15  Score=101.84  Aligned_cols=71  Identities=20%  Similarity=0.195  Sum_probs=58.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcCh-HHHHHHHh--cCCccCCeEeEEEeCCC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEE-VVADRVSR--RSHEICGQQVAIDSATP  175 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~-~~a~~A~~--~~~~~~g~~i~v~~a~~  175 (234)
                      ..+||+|||+.+|+++|+++|++||+|.+|.|++.   ++||||.|.+. ++|..|+.  ++..+.++.+.|.++..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~---kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG---AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT---CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC---CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            44599999999999999999999999999999864   79999999986 67777774  55566666666666543

>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=99.52  E-value=2.3e-14  Score=97.01  Aligned_cols=63  Identities=13%  Similarity=0.280  Sum_probs=54.9

Q ss_pred             CCCCCEEEEeC--CCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh--cCCcc
Q 026724           98 QRIGKKIFVGR--LPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR--RSHEI  163 (234)
Q Consensus        98 ~~~~~~l~v~n--l~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~  163 (234)
                      ..++.+|||.|  ||.++|+++|+++|++||.|..|.++++   ++||||+|.+.++|.+|+.  ++..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~---k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN---KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT---CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC---ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            45678899955  9999999999999999999999988864   7899999999999999984  55544

>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=99.51  E-value=8.7e-16  Score=104.75  Aligned_cols=72  Identities=15%  Similarity=0.164  Sum_probs=65.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee-cCCC-CcceEEEEEcChHHHHHHH--hcCCccCCeEeEEEeC
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRTG-HRGFGFVTFAEEVVADRVS--RRSHEICGQQVAIDSA  173 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~-~~g~afV~f~~~~~a~~A~--~~~~~~~g~~i~v~~a  173 (234)
                      ..++|.+++.+++|++|+++|++||+|.+|.|+ ..++ ++|+|||+|.+.++|.+|+  +++..++|++|+|++.
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            358888899999999999999999999999998 4456 9999999999999999998  4788999999999985

>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=99.49  E-value=2.7e-14  Score=92.55  Aligned_cols=72  Identities=13%  Similarity=0.218  Sum_probs=61.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeE-eEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQ-VAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~-i~v~~a~~~  176 (234)
                      .+.|+|.+||++++++.| ++|++||.|.++.+.+   .++||||+|.+.++|++|| +++..|+|+. |.|..+..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~---~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN---TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS---SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCCH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC---CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCCh
Confidence            567999999999987655 5799999999998865   3799999999999999999 4788999984 578877654

>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=99.49  E-value=5.2e-14  Score=105.55  Aligned_cols=79  Identities=37%  Similarity=0.574  Sum_probs=69.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCCC-CcceEEEEEcChHHHHHHHh-cCCccCCeEeEEEeCCCC
Q 026724          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRTG-HRGFGFVTFAEEVVADRVSR-RSHEICGQQVAIDSATPL  176 (234)
Q Consensus       101 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~~-~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~a~~~  176 (234)
                      .++|||+|||+++|+++|+++|++||.|.++.++  ..++ ++|||||+|.+.++|.+|+. ....+..+.+.+....+.
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            4689999999999999999999999999999988  4566 89999999999999999985 566888999998887666


Q ss_pred             CCC
Q 026724          177 DDA  179 (234)
Q Consensus       177 ~~~  179 (234)
                      ...
T Consensus        86 ~~~   88 (183)
T d1u1qa_          86 EDS   88 (183)
T ss_dssp             TGG
T ss_pred             ccc
Confidence            543

>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=99.47  E-value=1.2e-13  Score=93.11  Aligned_cols=80  Identities=24%  Similarity=0.329  Sum_probs=67.0

Q ss_pred             CCCCCEEEEeCC--CCCC---------CHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH--hcCCccC
Q 026724           98 QRIGKKIFVGRL--PQEA---------TAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS--RRSHEIC  164 (234)
Q Consensus        98 ~~~~~~l~v~nl--~~~~---------~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~--~~~~~~~  164 (234)
                      ...+++|+|.||  |.++         .+++|++.|++||.|..|.+..+. .+||+||+|++.++|.+|+  +++..++
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~-~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH-PDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC-TTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC-CccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            456889999999  5432         236899999999999999887332 6899999999999999998  4788999


Q ss_pred             CeEeEEEeCCCCCC
Q 026724          165 GQQVAIDSATPLDD  178 (234)
Q Consensus       165 g~~i~v~~a~~~~~  178 (234)
                      |+.|.|.++.++..
T Consensus        84 gr~i~v~~~~g~~~   97 (99)
T d2dita1          84 GRQITAQAWDGTTD   97 (99)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CEEEEEEEeCCcCC
Confidence            99999999987654

>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=99.40  E-value=1.3e-13  Score=91.31  Aligned_cols=49  Identities=20%  Similarity=0.390  Sum_probs=45.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.||+|||||||+|.+.++|++||++++.|+|+.|.|+++.++..
T Consensus        40 i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          40 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCC
T ss_pred             eccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCCCCC
Confidence            5789999999999999999999999999988999999999999987654

>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=99.31  E-value=1.1e-12  Score=85.39  Aligned_cols=49  Identities=24%  Similarity=0.388  Sum_probs=44.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|++++|||||+|.+.++|++||+  ++..|+|++|+|.+|.++..
T Consensus        31 i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~   81 (83)
T d1x5ta1          31 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   81 (83)
T ss_dssp             ECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             EEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCc
Confidence            46899999999999999999999999994  68899999999999987643

>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=99.30  E-value=1.4e-12  Score=88.63  Aligned_cols=76  Identities=18%  Similarity=0.302  Sum_probs=63.2

Q ss_pred             CCCEEEEeCC--CCCC--------CHHHHHHHHhhcCceeEEEeecC--C--C-CcceEEEEEcChHHHHHHH--hcCCc
Q 026724          100 IGKKIFVGRL--PQEA--------TAEDLRRYFSRFGRILDVYVPKR--T--G-HRGFGFVTFAEEVVADRVS--RRSHE  162 (234)
Q Consensus       100 ~~~~l~v~nl--~~~~--------~~~~l~~~f~~~G~v~~~~~~~~--~--~-~~g~afV~f~~~~~a~~A~--~~~~~  162 (234)
                      +++.|.|.||  +..+        ..+||++.|++||.|++|.|+++  +  . ..|++||+|.+.++|.+|+  +++..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            5788999999  5544        23578999999999999999832  2  1 4689999999999999998  57889


Q ss_pred             cCCeEeEEEeCCC
Q 026724          163 ICGQQVAIDSATP  175 (234)
Q Consensus       163 ~~g~~i~v~~a~~  175 (234)
                      ++||.|.|.+..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999754

>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=99.28  E-value=2.6e-12  Score=84.75  Aligned_cols=48  Identities=31%  Similarity=0.534  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|+++||||||+|.+.++|++||.  +++.|+|++|.|.+|.++.
T Consensus        37 i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          37 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             CCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             cccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            57899999999999999999999999994  7889999999999998654

>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=99.28  E-value=4.6e-13  Score=85.95  Aligned_cols=44  Identities=32%  Similarity=0.546  Sum_probs=41.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      |++|+.|++|||||||+|++.++|++||+ +++.|+|+.|.|+.|
T Consensus        32 i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             EECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             eecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            57899999999999999999999999995 788999999999876

>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=99.26  E-value=2e-12  Score=82.47  Aligned_cols=44  Identities=32%  Similarity=0.569  Sum_probs=40.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      |++|+.|+++||||||+|.+.++|++||+ +++.|+|+.|.|+.|
T Consensus        31 i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          31 LKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             cccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            67899999999999999999999999995 678999999999764

>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=99.26  E-value=2.9e-12  Score=85.24  Aligned_cols=49  Identities=31%  Similarity=0.585  Sum_probs=44.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|.|++|+|++|.++..
T Consensus        41 ~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          41 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             CCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             eeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            57899999999999999999999999994  78899999999999987653

>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=99.26  E-value=1.6e-12  Score=85.59  Aligned_cols=47  Identities=17%  Similarity=0.259  Sum_probs=43.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.||++||||||+|.+.++|++|+.  ++..|.|+.|+|+||.++
T Consensus        39 i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          39 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             ccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            46899999999999999999999999994  788999999999999865

>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=99.26  E-value=2.1e-12  Score=85.37  Aligned_cols=48  Identities=19%  Similarity=0.375  Sum_probs=43.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|+|+.|.|.+|.++.
T Consensus        40 i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          40 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             ccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            46789999999999999999999999995  6789999999999998764

>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=99.26  E-value=6.9e-12  Score=84.36  Aligned_cols=50  Identities=24%  Similarity=0.349  Sum_probs=45.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|+|++|+|.++.++...
T Consensus        40 i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             ecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCcc
Confidence            67899999999999999999999999994  678999999999999876543

>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=99.25  E-value=3.2e-12  Score=86.58  Aligned_cols=49  Identities=37%  Similarity=0.636  Sum_probs=45.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.|+.+||||||+|.+.++|++||+ +++.|+|+.|.|++|.++++
T Consensus        52 i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          52 VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE  101 (103)
T ss_dssp             EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCC
T ss_pred             ecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcccCC
Confidence            57899999999999999999999999994 78899999999999988765

>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=99.25  E-value=3e-12  Score=83.09  Aligned_cols=46  Identities=17%  Similarity=0.296  Sum_probs=42.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.||++||||||+|.+.++|++||  ++++.|.|++|+|.+|.|
T Consensus        34 i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          34 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            5789999999999999999999999999  478899999999999865

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=2.5e-12  Score=83.87  Aligned_cols=45  Identities=33%  Similarity=0.619  Sum_probs=41.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.||++||||||+|.+.++|++||+ +++.|+|+.|+|+.|.
T Consensus        38 i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          38 VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             ecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            56899999999999999999999999995 7889999999999885

>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=99.23  E-value=2.2e-12  Score=82.18  Aligned_cols=44  Identities=32%  Similarity=0.561  Sum_probs=40.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      |++|+.|+++||||||+|.+.++|++||+ +.+.|+|+.|.|+.|
T Consensus        31 i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             ccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            68999999999999999999999999996 578999999999865

>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=99.22  E-value=3.9e-12  Score=82.14  Aligned_cols=45  Identities=13%  Similarity=0.260  Sum_probs=41.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeecc
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~   45 (234)
                      |++|+.|++++|||||+|.++++|++||+  ++..|.|++|+|.++.
T Consensus        32 i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          32 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            57899999999999999999999999995  6889999999999984

>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=99.20  E-value=4.7e-12  Score=82.74  Aligned_cols=48  Identities=19%  Similarity=0.421  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.||++||||||+|.++++|++|+.  +++.|.|++|.|.+|.+..
T Consensus        33 i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          33 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             EECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             eeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            46899999999999999999999999995  6889999999999997643

>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=99.19  E-value=3.4e-12  Score=86.16  Aligned_cols=47  Identities=21%  Similarity=0.454  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~   47 (234)
                      |++|+.||+|||||||+|.+.++|++|| ++++.|.|++|.|+++.++
T Consensus        50 i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          50 IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             ECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             eeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCCC
Confidence            5789999999999999999999999999 5889999999999988653

>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=99.19  E-value=6.7e-12  Score=84.87  Aligned_cols=49  Identities=16%  Similarity=0.325  Sum_probs=44.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+.||++||||||+|.+.++|++||+  +++.|.|++|+|+++.++.+
T Consensus        50 ~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          50 VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             eeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            36789999999999999999999999994  78899999999999988764

>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=99.18  E-value=1.7e-11  Score=81.55  Aligned_cols=49  Identities=27%  Similarity=0.526  Sum_probs=42.6

Q ss_pred             CCCCCC-CCCccceEEEEEcCHHHHHHHHh---cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQG-SKAHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~-tg~srG~aFV~F~~~e~A~~Al~---~~~~i~gr~i~v~~a~~~~~   49 (234)
                      |++|+. ||++||||||+|.+.++|++||.   ++..|+|++|.|.||.++..
T Consensus        40 i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          40 LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             CCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             EEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCCC
Confidence            567754 89999999999999999999994   56789999999999987643

>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=99.17  E-value=1.5e-11  Score=81.73  Aligned_cols=48  Identities=23%  Similarity=0.269  Sum_probs=43.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..|+|++|.|.|+....
T Consensus        39 i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          39 MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK   88 (93)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             cccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            46899999999999999999999999994  7889999999999986543

>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=99.17  E-value=2.2e-11  Score=82.41  Aligned_cols=48  Identities=25%  Similarity=0.335  Sum_probs=42.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHhc-CceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~~-~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.||+|||||||+|.+.++|++||+. .+.|+|++|.|+++..+.
T Consensus        42 i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          42 VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGA   90 (103)
T ss_dssp             ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTTC
T ss_pred             ccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCCCC
Confidence            578999999999999999999999999963 458999999999987653

>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=99.16  E-value=1.3e-11  Score=79.98  Aligned_cols=46  Identities=22%  Similarity=0.388  Sum_probs=42.3

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+.+++++|||||+|.+.++|++|++  +++.|.|++|+|.+|.|
T Consensus        34 i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          34 LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46789999999999999999999999994  78999999999999875

>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=99.14  E-value=3.6e-11  Score=81.00  Aligned_cols=49  Identities=16%  Similarity=0.263  Sum_probs=44.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +++|+.|++++|||||+|.+.++|++||+  ++..|.|++|+|.+|.++..
T Consensus        48 ~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          48 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             CCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             EeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            46789999999999999999999999994  78899999999999987543

>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=99.14  E-value=3.1e-11  Score=86.19  Aligned_cols=50  Identities=20%  Similarity=0.371  Sum_probs=44.7

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+.|+++||||||+|.+.++|++||+  +++.|+|+.|+|.++.++...
T Consensus        74 i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~~  125 (139)
T d1u6fa1          74 IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             cccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            46789999999999999999999999994  788999999999999866543

>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=99.13  E-value=4.6e-11  Score=78.04  Aligned_cols=44  Identities=23%  Similarity=0.339  Sum_probs=37.8

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      ++.++++||||||+|.+.++|++||+ +++.|+|+.|+|.++.++
T Consensus        41 ~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          41 QKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             CC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECCCC
T ss_pred             cCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEcCCC
Confidence            56799999999999999999999995 788999999999999765

>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=99.12  E-value=2.8e-11  Score=79.82  Aligned_cols=49  Identities=31%  Similarity=0.607  Sum_probs=44.0

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +++++.+++++|||||+|+++++|++||+  +++.|.|++|.|++|.++..
T Consensus        37 ~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          37 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             eccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            36788999999999999999999999994  78899999999999987654

>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=99.11  E-value=4.7e-11  Score=76.53  Aligned_cols=45  Identities=18%  Similarity=0.202  Sum_probs=39.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      |++|+ +++++|||||+|.+.++|++|++  ++..|.|++|+|+++.+
T Consensus        32 i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_          32 VHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             ESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            35665 79999999999999999999994  78899999999999863

>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=99.10  E-value=3.3e-11  Score=77.84  Aligned_cols=45  Identities=16%  Similarity=0.248  Sum_probs=35.0

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      +++..++++||||||+|.+.++|++|+.  ++..|.|++|.|+++.|
T Consensus        34 ~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          34 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5677889999999999999999999994  78899999999999875

>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=99.10  E-value=1.6e-11  Score=83.21  Aligned_cols=48  Identities=21%  Similarity=0.429  Sum_probs=43.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.||++||||||+|.+.++|++||+  +++.|.|++|.|+++.++.
T Consensus        40 i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             cccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            46789999999999999999999999994  6889999999999987653

>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=99.09  E-value=2.4e-11  Score=79.22  Aligned_cols=44  Identities=16%  Similarity=0.337  Sum_probs=39.2

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCC--cEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG--STVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~g--r~i~v~~a   44 (234)
                      |++|+.|+++||||||+|.+.++|++||+  ++..+.|  ++|.|+||
T Consensus        38 ~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          38 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             eecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            46899999999999999999999999995  6777766  88999986

>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=99.09  E-value=4.6e-11  Score=75.93  Aligned_cols=44  Identities=36%  Similarity=0.594  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      +++++.|+.++|||||+|.+.++|++||+ +++.|+|++|+|++|
T Consensus        31 ~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             eeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            46788999999999999999999999995 788999999999876

>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=99.08  E-value=3.8e-11  Score=77.13  Aligned_cols=44  Identities=34%  Similarity=0.662  Sum_probs=40.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a   44 (234)
                      ++.|+.|++++|||||+|.+.++|++|++ +++.|+|++|.|+.|
T Consensus        34 ~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          34 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             cccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            35788999999999999999999999995 788999999999876

>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=99.07  E-value=4e-11  Score=79.18  Aligned_cols=45  Identities=18%  Similarity=0.409  Sum_probs=40.3

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~   47 (234)
                      .+..||++||||||+|.+.++|++||+ +++.|.|++|.|.+|..+
T Consensus        46 ~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          46 VDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             CEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCS
T ss_pred             eecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecCCC
Confidence            456789999999999999999999994 788999999999998754

>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=99.06  E-value=3.9e-11  Score=78.23  Aligned_cols=46  Identities=15%  Similarity=0.376  Sum_probs=39.2

Q ss_pred             CCCCCCC---CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            2 PKDQGSK---AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         2 ~rD~~tg---~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ++|+.++   +|||||||+|++.++|++||+  +++.|+|++|.|+++.+.
T Consensus        31 ~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          31 SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             EEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             ecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4565554   689999999999999999994  688999999999998643

>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=99.05  E-value=1.9e-10  Score=77.75  Aligned_cols=47  Identities=23%  Similarity=0.470  Sum_probs=40.8

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCCCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      +..++++||||||+|.+.++|++|+ ++++.|+|+.|+|++|.++...
T Consensus        50 ~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~~~~~~   97 (104)
T d1wi8a_          50 PSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             SSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCCC
T ss_pred             eccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            3468999999999999999999888 4788999999999999876543

>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=99.04  E-value=8.2e-11  Score=76.29  Aligned_cols=41  Identities=29%  Similarity=0.482  Sum_probs=37.8

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEE
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVV   41 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v   41 (234)
                      |++|+.|+++||||||+|.+.++|++||.  ++..|+|++|+|
T Consensus        41 i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          41 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            46789999999999999999999999994  788999999987

>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=99.02  E-value=7.3e-11  Score=76.89  Aligned_cols=44  Identities=27%  Similarity=0.427  Sum_probs=38.9

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCC--cEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG--STVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~g--r~i~v~~a   44 (234)
                      |++|+.|+++||||||+|.+.++|++|++  ++..|.|  ++|.|.||
T Consensus        38 i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          38 ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             cccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            46799999999999999999999999994  7888987  56999886

>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=99.01  E-value=3.2e-10  Score=75.71  Aligned_cols=49  Identities=16%  Similarity=0.381  Sum_probs=42.6

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--c------CceeCCcEEEEeeccCCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--D------THELGGSTVVVDRATPKED   49 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~------~~~i~gr~i~v~~a~~~~~   49 (234)
                      +++|+.+++++|||||+|.+.++|++||+  +      +..|.|+.|+|.++.++.+
T Consensus        40 ~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          40 VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             CCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             eccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCCc
Confidence            46788999999999999999999999995  2      4578999999999987643

>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=99.00  E-value=1.7e-10  Score=75.75  Aligned_cols=46  Identities=22%  Similarity=0.445  Sum_probs=39.2

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++|+  +.+||||||+|++.++|++||+  ++..|+|++|.|.++.++.+
T Consensus        41 ~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~   88 (89)
T d1cvja2          41 VCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   88 (89)
T ss_dssp             CCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTT
T ss_pred             Eeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            4555  4589999999999999999995  67899999999999987643

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=1.2e-10  Score=78.42  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=42.7

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +.|..+++++|||||+|.+.++|++||+  ++..|.|++|.|.+|.++..
T Consensus        51 ~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          51 QFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             EEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             ecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            4567789999999999999999999994  68899999999999987654

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=5.6e-10  Score=74.27  Aligned_cols=50  Identities=22%  Similarity=0.316  Sum_probs=41.3

Q ss_pred             CCCCC-CCCCccceEEEEEcCHHHHHHHHhc----CceeCCcEEEEeeccCCCCC
Q 026724            1 MPKDQ-GSKAHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         1 l~rD~-~tg~srG~aFV~F~~~e~A~~Al~~----~~~i~gr~i~v~~a~~~~~~   50 (234)
                      |++|+ .++++||||||+|.+.++|.+|+..    ...+.|++|.|.||.++...
T Consensus        34 ~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          34 VYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             CCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             EeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCC
Confidence            46675 5799999999999999999999953    34668999999999876543

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=1.7e-10  Score=75.64  Aligned_cols=45  Identities=27%  Similarity=0.426  Sum_probs=40.5

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHhcCceeCCcEEEEeeccCCCCC
Q 026724            6 GSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDD   50 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~~~~~i~gr~i~v~~a~~~~~~   50 (234)
                      .+..++|||||+|++.++|++||++++.|+|++|.|.++.++...
T Consensus        37 ~~~~~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          37 IPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCSSCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCCC
T ss_pred             EeeccCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCCCCCC
Confidence            456789999999999999999999999999999999999876544

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=3.6e-10  Score=76.41  Aligned_cols=48  Identities=17%  Similarity=0.216  Sum_probs=42.2

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (234)
                      +.+..+++++|||||+|+++++|++|++ +++.|.+|.|.|.++.+++.
T Consensus        48 ~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~~~~   96 (104)
T d1wg5a_          48 LPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEV   96 (104)
T ss_dssp             CCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTTS
T ss_pred             EEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCHHHh
Confidence            4566789999999999999999999995 78899999999999876643

>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=98.95  E-value=5.9e-10  Score=73.24  Aligned_cols=46  Identities=20%  Similarity=0.271  Sum_probs=39.4

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      |++|+.++  +|||||+|++.++|++|+.  +++.|.|+.|+|.+|.++.
T Consensus        40 i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          40 MITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             EECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             eecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            35676654  8999999999999999994  7889999999999997654

>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=98.93  E-value=3.5e-10  Score=73.53  Aligned_cols=43  Identities=16%  Similarity=0.249  Sum_probs=37.8

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeecc
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRAT   45 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~   45 (234)
                      ++| .++++||||||+|.+.++|++||+ ++..|.|+.|.|.+..
T Consensus        39 ~~~-~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          39 RRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             EEC-TTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             eee-ccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            344 479999999999999999999995 6889999999999864

>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=98.92  E-value=7.1e-10  Score=73.33  Aligned_cols=45  Identities=20%  Similarity=0.414  Sum_probs=39.0

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++|+  +.+||||||+|.+.++|++||.  ++..|+|+.|.|++|.++.
T Consensus        44 ~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          44 IFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             ECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             cccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            4554  3489999999999999999994  7889999999999998764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.91  E-value=3.7e-10  Score=73.58  Aligned_cols=42  Identities=17%  Similarity=0.276  Sum_probs=37.5

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeec
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a   44 (234)
                      .+..+++++|||||+|++.++|++||+  +++.|.||+|+|.++
T Consensus        43 ~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          43 KYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             EECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             EeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            455689999999999999999999994  788999999999864

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=98.91  E-value=4.5e-10  Score=74.75  Aligned_cols=46  Identities=22%  Similarity=0.319  Sum_probs=40.9

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++.+++++|||||+|.+.++|++|++  +++.|+|++|.|.++.++..
T Consensus        46 ~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          46 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             eeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            34678999999999999999999995  67899999999999987754

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=3.4e-10  Score=76.21  Aligned_cols=47  Identities=13%  Similarity=0.081  Sum_probs=40.5

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh-cCceeCCcEEEEeeccCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++|. +++++|||||+|.+.++|++||+ +++.|.||.|+|.++.++..
T Consensus        47 ~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~~~~~   94 (102)
T d1weza_          47 EIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             EESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCCC
T ss_pred             EEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            3444 58999999999999999999994 78899999999999887653

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=5.4e-10  Score=71.76  Aligned_cols=48  Identities=19%  Similarity=0.263  Sum_probs=40.9

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHHh--cCc-eeCCcEEEEeeccCCCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTH-ELGGSTVVVDRATPKED   49 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~-~i~gr~i~v~~a~~~~~   49 (234)
                      +.+..+.++||||||+|.+.++|++||+  ++. .|+|++|.|+++.++..
T Consensus        28 i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          28 PLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             EEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            4456677899999999999999999994  564 69999999999988654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=7.9e-10  Score=74.52  Aligned_cols=44  Identities=16%  Similarity=0.224  Sum_probs=39.3

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~   46 (234)
                      .+..+|+++|||||+|.+.++|++|| ++++.|.|+.|.|.++..
T Consensus        42 ~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1          42 LVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             EeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            45678999999999999999999999 478899999999998754

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=8e-10  Score=74.55  Aligned_cols=43  Identities=9%  Similarity=0.237  Sum_probs=38.1

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeec
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a   44 (234)
                      |++| .|+++||||||+|.+.++|.+|+.  +++.|+|++|.|+++
T Consensus        59 I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          59 VCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             ECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             eecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3455 589999999999999999999994  799999999999875

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=9.2e-10  Score=71.96  Aligned_cols=46  Identities=13%  Similarity=0.248  Sum_probs=39.8

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCC
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++..++++||||||+|.+.++|++||  ++++.|.|++|.|+++..+.
T Consensus        32 ~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          32 KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             eeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            34456789999999999999999999  47889999999999986544

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=8.7e-10  Score=71.77  Aligned_cols=45  Identities=24%  Similarity=0.398  Sum_probs=39.5

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ..++++||||||+|.+.++|.+||.  ++..|.|+.|.|.++.|+..
T Consensus        38 ~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1          38 ERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             EEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            3457899999999999999999994  78899999999999987654

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.84  E-value=1.6e-09  Score=70.93  Aligned_cols=42  Identities=10%  Similarity=0.269  Sum_probs=36.1

Q ss_pred             CCCCCCCCCcc---ceEEEEEcCHHHHHHHH--hcCceeCCcEEEEe
Q 026724            1 MPKDQGSKAHR---GIGFITFASADSVENLM--VDTHELGGSTVVVD   42 (234)
Q Consensus         1 l~rD~~tg~sr---G~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~   42 (234)
                      |++|+.|+.++   |||||+|++.++|++||  +|+..|+|++|+|.
T Consensus        43 i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          43 INNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             EECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             EeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            46788777665   99999999999999999  47899999999873

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.83  E-value=5.4e-10  Score=73.60  Aligned_cols=46  Identities=20%  Similarity=0.251  Sum_probs=39.9

Q ss_pred             CCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            4 DQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         4 D~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .+.|++++|||||+|++.++|++|+.  +++.|+|+.|.|.+|.++.+
T Consensus        39 ~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~~   86 (91)
T d1nu4a_          39 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   86 (91)
T ss_dssp             CCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             EeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCch
Confidence            34567899999999999999999994  68899999999999986543

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.83  E-value=2.4e-09  Score=71.41  Aligned_cols=40  Identities=15%  Similarity=0.433  Sum_probs=35.7

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      .+||||||+|++.++|++||.  +++.|.|++|+|.++.++.
T Consensus        48 i~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          48 VHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             EETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             EeCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            378999999999999999994  7889999999999997643

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.81  E-value=1.4e-09  Score=68.88  Aligned_cols=43  Identities=14%  Similarity=0.210  Sum_probs=37.9

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~   47 (234)
                      ..++++||||||+|.+.++|++|+  +++..|.|++|.|+++...
T Consensus        27 ~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          27 CFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             eeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            346789999999999999999999  4788999999999998643

>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=98.77  E-value=2e-09  Score=73.80  Aligned_cols=43  Identities=12%  Similarity=0.163  Sum_probs=38.2

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ..++.+||||||+|.+.++|++||.  +++.|+|+.|.|.++.+.
T Consensus        40 ~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1          40 GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             ECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             cccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4567899999999999999999994  788999999999998653

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.75  E-value=9.3e-10  Score=75.32  Aligned_cols=46  Identities=17%  Similarity=0.238  Sum_probs=40.5

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeeccCC
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPK   47 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~~~   47 (234)
                      +.+..+|+++|||||+|.+.++|++|| ++++.|+||.|.|..+..+
T Consensus        51 ~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~~~   97 (112)
T d1wela1          51 IAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKK   97 (112)
T ss_dssp             EEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECHH
T ss_pred             eecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcChH
Confidence            356678999999999999999999999 5888999999999987643

>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=98.74  E-value=1e-09  Score=68.90  Aligned_cols=39  Identities=15%  Similarity=0.348  Sum_probs=34.5

Q ss_pred             CCCCCCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEE
Q 026724            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTV   39 (234)
Q Consensus         1 l~rD~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i   39 (234)
                      +++++.|++++|||||+|.+.++|++|++  ++..|.|+.|
T Consensus        30 ~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1          30 AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             cccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            35788999999999999999999999994  6778888876

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.73  E-value=5.6e-09  Score=69.13  Aligned_cols=43  Identities=14%  Similarity=0.285  Sum_probs=37.7

Q ss_pred             CCCCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         5 ~~tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ..+..+||||||+|++.++|++||+  +++.|.|++|+|++|.+.
T Consensus        47 ~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          47 KNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             cccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            3456789999999999999999994  788999999999998754

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=3.5e-09  Score=67.67  Aligned_cols=41  Identities=15%  Similarity=0.311  Sum_probs=36.6

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      ..+.+|||||+|.+.++|++|++  ++..|+|++|+|.|+.++
T Consensus        35 ~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          35 MDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             EETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             eccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            35678999999999999999994  788999999999999754

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=7.5e-10  Score=72.72  Aligned_cols=43  Identities=19%  Similarity=0.324  Sum_probs=37.8

Q ss_pred             CCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeecc
Q 026724            3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRAT   45 (234)
Q Consensus         3 rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a~   45 (234)
                      .|..++++||||||+|++.++|++|+ +++..|.|+.|+|+++.
T Consensus        40 ~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          40 LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             EECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBCTT
T ss_pred             eecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECCCC
Confidence            45678899999999999999999999 47889999999997543

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=1.6e-08  Score=66.99  Aligned_cols=39  Identities=18%  Similarity=0.387  Sum_probs=35.0

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      .||||||+|.+.++|++||+  ++..|.|++|+|.|+.++.
T Consensus        53 ~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          53 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            48999999999999999994  7889999999999987643

>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=98.63  E-value=3.1e-09  Score=71.25  Aligned_cols=41  Identities=22%  Similarity=0.397  Sum_probs=36.2

Q ss_pred             CCCCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            6 GSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      .+++++|||||+|.+.++|++||  +|+..|.|+++.|.++.|
T Consensus        54 ~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          54 SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            47899999999999999999999  488999999988876654

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=1.7e-08  Score=65.75  Aligned_cols=40  Identities=15%  Similarity=0.310  Sum_probs=34.6

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCcee-CCcEEEEeeccC
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHEL-GGSTVVVDRATP   46 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i-~gr~i~v~~a~~   46 (234)
                      +++++|||||+|++.++|.+|+.  ++..| +|++|+|.++.+
T Consensus        44 ~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          44 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             eecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            46789999999999999999994  57777 689999999865

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.62  E-value=1.6e-08  Score=63.81  Aligned_cols=41  Identities=15%  Similarity=0.182  Sum_probs=34.4

Q ss_pred             CCCCCCCCccceEEEEEcCHHHHHHHH-hcCceeCCcEEEEeec
Q 026724            2 PKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRA   44 (234)
Q Consensus         2 ~rD~~tg~srG~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a   44 (234)
                      ++|+.  ..++||||+|++.++|++|| ++++.|+|++|.|..+
T Consensus        33 ~~~~~--~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          33 ADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             EECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             Eeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            45554  34579999999999999999 4788999999999865

>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=98.60  E-value=2.8e-08  Score=66.12  Aligned_cols=43  Identities=14%  Similarity=0.326  Sum_probs=37.8

Q ss_pred             CCCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         7 tg~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      ++.++|||||+|+++++|.+|+.  ++..|+||+|.|.++.++..
T Consensus        53 ~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          53 DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             TTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             CCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcCC
Confidence            35678999999999999999994  78899999999999877653

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.60  E-value=3.2e-08  Score=66.98  Aligned_cols=38  Identities=13%  Similarity=0.308  Sum_probs=34.2

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCC
Q 026724           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~   47 (234)
                      .||||||+|++.++|++||+  ++..|.|+.|+|+++...
T Consensus        39 ~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1          39 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            48999999999999999994  788999999999998644

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.60  E-value=2.4e-08  Score=67.06  Aligned_cols=42  Identities=14%  Similarity=-0.023  Sum_probs=37.3

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .++++||||+|.+.++|++|++  ++..|.|++|+|.|+.++..
T Consensus        43 ~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   86 (104)
T d1weya_          43 FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI   86 (104)
T ss_dssp             ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSC
T ss_pred             ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCC
Confidence            4689999999999999999995  67799999999999976654

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.57  E-value=1.9e-08  Score=65.17  Aligned_cols=40  Identities=28%  Similarity=0.367  Sum_probs=35.9

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++||||||+|++.++|++|+.  ++..|+|++|+|++|.+..
T Consensus        42 ~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          42 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            568999999999999999994  7889999999999997653

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.49  E-value=7.5e-08  Score=65.28  Aligned_cols=41  Identities=5%  Similarity=0.003  Sum_probs=36.1

Q ss_pred             CCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCC
Q 026724            8 KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~   48 (234)
                      .++||||||+|.+.++|++||  +++..|.|++|.|+|+....
T Consensus        43 ~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          43 PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            457899999999999999999  47889999999999986543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=2.3e-07  Score=60.14  Aligned_cols=40  Identities=15%  Similarity=0.281  Sum_probs=34.6

Q ss_pred             CccceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++++||||+|.+.++|++|+.    +...|.|++|+|.++..+.
T Consensus        42 ~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          42 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            568999999999999999994    3568999999999987654

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.37  E-value=3.6e-07  Score=61.15  Aligned_cols=40  Identities=15%  Similarity=0.274  Sum_probs=34.5

Q ss_pred             CccceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++||||||+|++.++|++||.    +...+.|++|+|.++..++
T Consensus        49 ~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~   92 (104)
T d1wexa_          49 PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCc
Confidence            578999999999999999994    3457899999999997654

>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=98.34  E-value=3.2e-07  Score=61.37  Aligned_cols=46  Identities=20%  Similarity=0.338  Sum_probs=38.1

Q ss_pred             CCCCCCC--CCccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccC
Q 026724            1 MPKDQGS--KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATP   46 (234)
Q Consensus         1 l~rD~~t--g~srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~   46 (234)
                      |++++.+  ..++|++||+|.+.++|.+|+  +++..++||+|.|.+...
T Consensus        46 I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          46 IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             CCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECH
T ss_pred             EeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCH
Confidence            4555544  456799999999999999999  478899999999998753

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.34  E-value=1.2e-07  Score=60.51  Aligned_cols=42  Identities=17%  Similarity=0.109  Sum_probs=35.0

Q ss_pred             CCCCccceEEEEEcCHHHHHHHHh-cCceeCCcE-EEEeeccCC
Q 026724            6 GSKAHRGIGFITFASADSVENLMV-DTHELGGST-VVVDRATPK   47 (234)
Q Consensus         6 ~tg~srG~aFV~F~~~e~A~~Al~-~~~~i~gr~-i~v~~a~~~   47 (234)
                      .+++++|||||+|.++++|++||+ |+..|+|+. |.|..+..+
T Consensus        34 ~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1          34 VMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             EECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCCH
T ss_pred             EecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCCh
Confidence            456789999999999999999994 788999985 568776543

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.33  E-value=2.3e-07  Score=61.52  Aligned_cols=40  Identities=15%  Similarity=0.207  Sum_probs=34.7

Q ss_pred             CccceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++||||||+|++.++|.+||.    ++..|.|+.|.|.++..+.
T Consensus        53 ~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          53 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            568999999999999999994    4568999999999997554

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.33  E-value=2.7e-07  Score=62.21  Aligned_cols=41  Identities=12%  Similarity=0.161  Sum_probs=34.0

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCcee--CCcEEEEeeccCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHEL--GGSTVVVDRATPKED   49 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i--~gr~i~v~~a~~~~~   49 (234)
                      +++|||||+|++.++|++||.  ++..|  .+++|+|.++.++..
T Consensus        43 ~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            478999999999999999994  67777  578899988876543

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.30  E-value=1.6e-07  Score=62.23  Aligned_cols=41  Identities=10%  Similarity=0.228  Sum_probs=35.6

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCCcEEEEeeccCCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (234)
                      .++|||||+|.+.++|++||+  ++..|.|+.|.|.++..+..
T Consensus        48 ~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          48 QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            357999999999999999994  78899999999999876543

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=98.30  E-value=2.8e-07  Score=59.03  Aligned_cols=36  Identities=11%  Similarity=0.186  Sum_probs=31.3

Q ss_pred             ccceEEEEEcCHHHHHHHHh--cCcee-CCcEEEEeecc
Q 026724           10 HRGIGFITFASADSVENLMV--DTHEL-GGSTVVVDRAT   45 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al~--~~~~i-~gr~i~v~~a~   45 (234)
                      .+|||||+|.+.++|++|+.  ++..| ++++|.|.||.
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          44 RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            57999999999999999994  66677 57899999985

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.30  E-value=1e-07  Score=61.74  Aligned_cols=39  Identities=13%  Similarity=0.227  Sum_probs=33.7

Q ss_pred             ccceEEEEEcCHHHHHHHH--hcCceeCCcEEEEeeccCCC
Q 026724           10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKE   48 (234)
Q Consensus        10 srG~aFV~F~~~e~A~~Al--~~~~~i~gr~i~v~~a~~~~   48 (234)
                      ++|||||+|++.++|++||  +++..|.|+.|.|.++..+.
T Consensus        34 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1          34 RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            4599999999999999999  47889999999988876543

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.26  E-value=4.8e-07  Score=59.70  Aligned_cols=40  Identities=23%  Similarity=0.344  Sum_probs=33.7

Q ss_pred             CccceEEEEEcCHHHHHHHHh--cCceeCC--cEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV--DTHELGG--STVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~--~~~~i~g--r~i~v~~a~~~~   48 (234)
                      ++|+||||+|.+.++|++|++  ++..|.|  ++|+|.|+.+..
T Consensus        51 ~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            468999999999999999994  6778876  589999987643

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.20  E-value=1.1e-06  Score=56.97  Aligned_cols=40  Identities=15%  Similarity=0.150  Sum_probs=34.0

Q ss_pred             CccceEEEEEcCHHHHHHHHh----cCceeCCcEEEEeeccCCC
Q 026724            9 AHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKE   48 (234)
Q Consensus         9 ~srG~aFV~F~~~e~A~~Al~----~~~~i~gr~i~v~~a~~~~   48 (234)
                      .+++||||+|++.++|++|+.    ++..+.|++|.|.++.+..
T Consensus        43 ~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1          43 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            467899999999999999995    3558999999999997543

>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=97.76  E-value=6.3e-05  Score=47.47  Aligned_cols=71  Identities=20%  Similarity=0.258  Sum_probs=55.7

Q ss_pred             CCCCEEEEeCCCCCCCH---------HHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHH-hcCCccCCeEe
Q 026724           99 RIGKKIFVGRLPQEATA---------EDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVS-RRSHEICGQQV  168 (234)
Q Consensus        99 ~~~~~l~v~nl~~~~~~---------~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i  168 (234)
                      ++.-+|.|.=+.+...+         .+|.+.|..||+|.-|+++.+     --.|+|.+-++|.+|+ +++.++.|+.|
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-----~mwVTF~dG~SAL~al~l~g~~v~G~~l   87 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----QMLVTFADSHSALSVLDVDGMKVKGRAV   87 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----EEEEECSCSHHHHHHHHGGGSEETTEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-----eEEEEECCcHHHHHHhccCCeEEcceEE
Confidence            34667878555433322         367888999999999999843     5899999999999999 58999999999


Q ss_pred             EEEeCC
Q 026724          169 AIDSAT  174 (234)
Q Consensus       169 ~v~~a~  174 (234)
                      +|....
T Consensus        88 ~It~~~   93 (95)
T d1ufwa_          88 KISGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEecCC
Confidence            997543

>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=97.52  E-value=4.9e-05  Score=50.03  Aligned_cols=27  Identities=11%  Similarity=0.332  Sum_probs=22.5

Q ss_pred             CCccceEEEEEcCHHHHHHHHh--cCcee
Q 026724            8 KAHRGIGFITFASADSVENLMV--DTHEL   34 (234)
Q Consensus         8 g~srG~aFV~F~~~e~A~~Al~--~~~~i   34 (234)
                      -.+|+||||+|.+.++|++|+.  ++..|
T Consensus        53 ~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          53 PPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             ccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3568899999999999999994  56555

>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=97.45  E-value=0.00045  Score=41.27  Aligned_cols=59  Identities=19%  Similarity=0.164  Sum_probs=48.6

Q ss_pred             HHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHhcC--CccCCeEeEEEeCC
Q 026724          116 EDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSRRS--HEICGQQVAIDSAT  174 (234)
Q Consensus       116 ~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~~--~~~~g~~i~v~~a~  174 (234)
                      +.|.+.|.+++.|.++.|...+...-.|-|...+..+|.-|+.+.  ..|..++|.|.++.
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 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345678899999999999854444457999999999999999654  49999999999875

>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=97.13  E-value=8.8e-05  Score=49.79  Aligned_cols=38  Identities=13%  Similarity=0.013  Sum_probs=27.6

Q ss_pred             CccceEEEEEcCH-HHHHHHHh--cCceeCCcEEEEeeccC
Q 026724            9 AHRGIGFITFASA-DSVENLMV--DTHELGGSTVVVDRATP   46 (234)
Q Consensus         9 ~srG~aFV~F~~~-e~A~~Al~--~~~~i~gr~i~v~~a~~   46 (234)
                      +.+|||||.|++. ++|.+|+.  ++..|.++.+.|.++..
T Consensus        45 ~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          45 RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            4589999999996 67888884  55566666666665543

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.00  E-value=0.0015  Score=41.48  Aligned_cols=73  Identities=12%  Similarity=0.080  Sum_probs=52.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCceeEEEee--cCC-C--CcceEEEEEcChHHHHHHHh--cCCccCC-----eEeE
Q 026724          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRT-G--HRGFGFVTFAEEVVADRVSR--RSHEICG-----QQVA  169 (234)
Q Consensus       102 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~--~~~-~--~~g~afV~f~~~~~a~~A~~--~~~~~~g-----~~i~  169 (234)
                      ++|.|+.||+++||+++.+.+...+.+......  +.+ +  .-.-|+|.|.+.++...-..  +++.+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            589999999999999999999999988877666  221 2  33569999999998777653  4553321     1345


Q ss_pred             EEeCC
Q 026724          170 IDSAT  174 (234)
Q Consensus       170 v~~a~  174 (234)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>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=96.02  E-value=0.023  Score=36.01  Aligned_cols=56  Identities=21%  Similarity=0.248  Sum_probs=44.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCceeEEEeecCCCCcceEEEEEcChHHHHHHHh
Q 026724           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRTGHRGFGFVTFAEEVVADRVSR  158 (234)
Q Consensus        98 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  158 (234)
                      .+.-..||.-..|..+...||.++|+.||.|.- ..+.+    --|||...+.++|+.+++
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIdd----TSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDD----TSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEET----TEEEEECSCHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEE-EEecC----ceEEEEecCHHHHHHHHH
Confidence            344556888899999999999999999998753 33344    369999999999988864

>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=90.37  E-value=0.14  Score=31.74  Aligned_cols=32  Identities=25%  Similarity=0.395  Sum_probs=28.4

Q ss_pred             eEEEEEcCHHHHHHHH-hcCceeCCcEEEEeec
Q 026724           13 IGFITFASADSVENLM-VDTHELGGSTVVVDRA   44 (234)
Q Consensus        13 ~aFV~F~~~e~A~~Al-~~~~~i~gr~i~v~~a   44 (234)
                      --+|+|.+-+.|-+|+ +++.++.|+.|.|...
T Consensus        60 ~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          60 QMLVTFADSHSALSVLDVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             EEEEECSCSHHHHHHHHGGGSEETTEEEEEECC
T ss_pred             eEEEEECCcHHHHHHhccCCeEEcceEEEEecC
Confidence            4689999999999999 5899999999999754

>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=82.78  E-value=1  Score=26.38  Aligned_cols=33  Identities=12%  Similarity=0.215  Sum_probs=29.0

Q ss_pred             eEEEEEcCHHHHHHHHhc--CceeCCcEEEEeecc
Q 026724           13 IGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (234)
Q Consensus        13 ~aFV~F~~~e~A~~Al~~--~~~i~gr~i~v~~a~   45 (234)
                      .|-|...+..+|.-|+.+  -+.|+.+.|.|.++.
T Consensus        37 ~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          37 KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            588999999999999976  449999999998875