Citrus Sinensis ID: 021295

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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-------240-------250-------260-------270-------280-------290-------300-------310----
Protein Sequence
MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
Secondary Structure (PSIPRED)
cccccccccccEEEEEEccHHHHHHHHHcccccccEEEEEEcccccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEcccHHHHHHHHHcccEEEcccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
EEccccccEEEEEEEEEccHHHHHHHHHccccccccEEEccEEccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHccccEEcccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mkdrktgqprgfgfvtyadpsvvdkVIEDthiingkqveikrtipkgavgskdfktkkifvggipssvnedEFKDFFMqfgdvqehqimrdhstsrsrgfgfitfDTEQAVDDLLAKGNKLELAGAQVevkkaepkkpnlpqpsyrrynnpkpaygsgfgdayggyggggfagggfggsggggggggyrssgaygvrgggyggygvggefggyggygggmgayrgepsslgysgryggfnrgydvtgdygglnesyggyggsgvgggggygggpsgydiglgssyggssggaffgsrggyggaggssryhpygr
Flexible Loop (DISEMBL)
mkdrktgqprgfgfvtyadpsvvDKVIEDthiingkqveikrtipkgavgskdfktkkifVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGaqvevkkaepkkpnlpqpsyrryNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGgyggaggssryhpygr
Low Complexity Region (SEG)
MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAygsgfgdayggyggggfagggfggsggggggggyrssgaygvrgggyggygvggefggyggygggmgayrgEPSSLGYSGRYGGFNRGYDVTGDygglnesyggyggsgvgggggygggpsgydiglgssyggssggaffgsrggyggaggssrYHPYGR
Disordered region (IsUnstruct)
**********GFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM********RGFGFITFDTEQAVDDLLAKGNKL*************************************FGDAYGGYGGG************************YGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYG*********************************************************
Disordered Region (DISOPRED)
MK*RKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQV********************IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV****************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
********PRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
Disordered Region (DISPRO)
MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK*AVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK**************PKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
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	314	2.2.26 [Sep-21-2011]
Q8W034	411	Heterogeneous nuclear rib	no	no	0.439	0.335	0.438	4e-32
O94432	474	Uncharacterized RNA-bindi	yes	no	0.417	0.276	0.426	1e-26
Q9VVE5	369	RNA-binding protein Musas	yes	no	0.445	0.379	0.436	1e-26
Q920Q6	346	RNA-binding protein Musas	yes	no	0.445	0.404	0.408	9e-26
Q99383	534	Nuclear polyadenylated RN	yes	no	0.417	0.245	0.433	1e-25
Q96DH6	328	RNA-binding protein Musas	yes	no	0.445	0.426	0.408	1e-25
P48809	421	Heterogeneous nuclear rib	no	no	0.429	0.320	0.401	2e-25
Q96EP5	407	DAZ-associated protein 1	no	no	0.429	0.331	0.390	5e-23
Q9JII5	406	DAZ-associated protein 1	no	no	0.429	0.332	0.390	8e-23
O43347	362	RNA-binding protein Musas	no	no	0.595	0.516	0.354	1e-22

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

 Score =  139 bits (349), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 68/155 (43%), Positives = 105/155 (67%), Gaps = 17/155 (10%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK------GAVGSKDF 54
           M+D+ TG+PRGFGFV ++DPSV+D+V+++ H I+ ++V++KR + +      G  G+ + 
Sbjct: 38  MRDKLTGRPRGFGFVIFSDPSVLDRVLQEKHSIDTREVDVKRAMSREEQQVSGRTGNLNT 97

Query: 55  ----------KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
                     KTKKIFVGG+P ++ ++EF+ +F  +G V +  IM D +T+R RGFGF++
Sbjct: 98  SRSSGGDAYNKTKKIFVGGLPPTLTDEEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVS 157

Query: 105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
           FD+E AVD +L K    +L+G QVEVK+A PK  N
Sbjct: 158 FDSEDAVDSVLHKTFH-DLSGKQVEVKRALPKDAN 191

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 =  120 bits (301), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 58/136 (42%), Positives = 89/136 (65%), Gaps = 5/136 (3%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           M+D  TG+ RGFGF+T+ +P  V++V+   H ++GK ++ KR IP+     +  KT K+F
Sbjct: 195 MRDSTTGRSRGFGFLTFKNPKCVNEVMSKEHHLDGKIIDPKRAIPR----EEQEKTAKMF 250

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGG+P    E+EF++FF QFG V +  +M D  T R RGFGF+T++ E AV+  +++   
Sbjct: 251 VGGVPGDCTEEEFRNFFNQFGRVLDATLMMDKDTGRPRGFGFVTYENESAVEATMSQP-Y 309

Query: 121 LELAGAQVEVKKAEPK 136
           + + G  VEVK+A PK
Sbjct: 310 ITIHGKPVEVKRATPK 325

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

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

 Score =  120 bits (301), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 62/142 (43%), Positives = 91/142 (64%), Gaps = 2/142 (1%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKGAVGSKDFKTKKI 59
           MKD  T + RGFGFVT++DP+ VDKV+   TH ++GK+V+ K   P+ A      +TKKI
Sbjct: 61  MKDPTTRRSRGFGFVTFSDPNSVDKVLTQGTHELDGKKVDPKVAFPRRAHPKMVTRTKKI 120

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           FVGG+ +    ++ K +F QFG +++  +M D  T+R RGFGF+TF +E  VD  + + +
Sbjct: 121 FVGGLSAPTTLEDVKSYFEQFGPIEDAMLMFDKQTNRHRGFGFVTFQSEDVVDK-VCEIH 179

Query: 120 KLELAGAQVEVKKAEPKKPNLP 141
             E+    VE KKA+PK+  LP
Sbjct: 180 FHEINNKMVECKKAQPKEVMLP 201

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

 Score =  117 bits (294), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 58/142 (40%), Positives = 90/142 (63%), Gaps = 2/142 (1%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKRTIPKGAVGSKDFKTKKI 59
           M+D  T + RGFGFVT+ADP+ VDKV+ +  H ++ K ++ K   P+ A      +TKKI
Sbjct: 53  MRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKI 112

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           FVGG+ ++   ++ K +F QFG V++  +M D +T+R RGFGF+TF+ E  V+  + + +
Sbjct: 113 FVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK-VCEIH 171

Query: 120 KLELAGAQVEVKKAEPKKPNLP 141
             E+    VE KKA+PK+   P
Sbjct: 172 FHEINNKMVECKKAQPKEVMFP 193

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|Q99383|HRP1_YEAST Nuclear polyadenylated RNA-binding protein 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HRP1 PE=1 SV=1

 Score =  117 bits (293), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 59/136 (43%), Positives = 90/136 (66%), Gaps = 5/136 (3%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           MKD  TG+ RGFGF+++  PS VD+V++  HI++GK ++ KR IP+        KT KIF
Sbjct: 191 MKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQD----KTGKIF 246

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGGI   V   EF++FF Q+G + + Q+M D  T +SRGFGF+T+D+  AV D + +   
Sbjct: 247 VGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV-DRVCQNKF 305

Query: 121 LELAGAQVEVKKAEPK 136
           ++    ++E+K+AEP+
Sbjct: 306 IDFKDRKIEIKRAEPR 321

RNA-binding protein, which is involved in the polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with the cleavage factor CFIA complex and the cleavage and polyadenylation factor (CPF) complex. May be involved in regulation of poly(A) site selection. Is involved in nonsense-mediated mRNA decay. Seems to bind to a RNA downstream sequence element (DSE) located 3' of a nonsense codon and may mark the transcript for decay.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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

 Score =  117 bits (293), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/142 (40%), Positives = 90/142 (63%), Gaps = 2/142 (1%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKRTIPKGAVGSKDFKTKKI 59
           M+D  T + RGFGFVT+ADP+ VDKV+ +  H ++ K ++ K   P+ A      +TKKI
Sbjct: 53  MRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKI 112

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           FVGG+ ++   ++ K +F QFG V++  +M D +T+R RGFGF+TF+ E  V+  + + +
Sbjct: 113 FVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK-VCEIH 171

Query: 120 KLELAGAQVEVKKAEPKKPNLP 141
             E+    VE KKA+PK+   P
Sbjct: 172 FHEINNKMVECKKAQPKEVMFP 193

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

 Score =  116 bits (291), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 90/137 (65%), Gaps = 2/137 (1%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKGAVGSKDFKTKKI 59
           MK+ ++G+ RGFGFVT+ADP+ V+ V+++  H ++G+ ++ K   P+     K     K+
Sbjct: 39  MKNNESGRSRGFGFVTFADPTNVNHVLQNGPHTLDGRTIDPKPCNPRTLQKPKKGGGYKV 98

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           F+GG+PS+V E + + FF ++G V E  IM D    +SRGFGF++F+ E +V+ +  +  
Sbjct: 99  FLGGLPSNVTETDLRTFFNRYGKVTEVVIMYDQEKKKSRGFGFLSFEEESSVEHVTNE-R 157

Query: 120 KLELAGAQVEVKKAEPK 136
            + L G QVE+KKAEP+
Sbjct: 158 YINLNGKQVEIKKAEPR 174

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|Q96EP5|DAZP1_HUMAN DAZ-associated protein 1 OS=Homo sapiens GN=DAZAP1 PE=1 SV=1

 Score =  108 bits (270), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/151 (39%), Positives = 87/151 (57%), Gaps = 16/151 (10%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKGAVG--------- 50
           MKD+ T Q RGFGFV + DP+ V  V+    H ++G+ ++ K   P+G            
Sbjct: 42  MKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGW 101

Query: 51  -----SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
                S + K+ KIFVGGIP +  E E +++F +FG V E  ++ D    R RGFGFITF
Sbjct: 102 QKGPRSDNSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF 161

Query: 106 DTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 136
           + EQ+VD  +   +  ++ G +VEVK+AEP+
Sbjct: 162 EDEQSVDQAV-NMHFHDIMGKKVEVKRAEPR 191

RNA-binding protein, which may be required during spermatogenesis.

Homo sapiens (taxid: 9606)

>sp|Q9JII5|DAZP1_MOUSE DAZ-associated protein 1 OS=Mus musculus GN=Dazap1 PE=2 SV=2

 Score =  107 bits (268), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 59/151 (39%), Positives = 86/151 (56%), Gaps = 16/151 (10%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKGAVG--------- 50
           MKD+ T Q RGFGFV + DP+ V  V+    H ++G+ ++ K   P+G            
Sbjct: 42  MKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGW 101

Query: 51  -----SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
                S   K+ KIFVGGIP +  E E +++F +FG V E  ++ D    R RGFGFITF
Sbjct: 102 QKGPRSDSSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF 161

Query: 106 DTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 136
           + EQ+VD  +   +  ++ G +VEVK+AEP+
Sbjct: 162 EDEQSVDQAV-NMHFHDIMGKKVEVKRAEPR 191

RNA-binding protein, which may be required during spermatogenesis.

Mus musculus (taxid: 10090)

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

 Score =  107 bits (266), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 67/189 (35%), Positives = 100/189 (52%), Gaps = 2/189 (1%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKRTIPKGAVGSKDFKTKKI 59
           M+D  T + RGFGFVT+ D + VDKV+ +  H ++ K ++ K   P+ A      +TKKI
Sbjct: 52  MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKI 111

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           FVGG+  +   ++ K +F QFG V +  +M D +T+R RGFGF+TF++E  V+  + + +
Sbjct: 112 FVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEIH 170

Query: 120 KLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGS 179
             E+    VE KKA+PK+   P  S R  +   P     F    G  G  GF    +   
Sbjct: 171 FHEINNKMVECKKAQPKEVMSPTGSARGRSRVMPYGMDAFMLGIGMLGYPGFQATTYASR 230

Query: 180 GGGGGGGGY 188
              G   GY
Sbjct: 231 SYTGLAPGY 239

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)

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	314
388500070	373	unknown [Lotus japonicus] gi|388508218|g	0.936	0.788	0.671	9e-83
359488807	2363	PREDICTED: nuclear pore membrane glycopr	0.770	0.102	0.687	1e-80
449446702	2257	PREDICTED: LOW QUALITY PROTEIN: nuclear	0.945	0.131	0.624	6e-80
356571134	374	PREDICTED: heterogeneous nuclear ribonuc	0.939	0.788	0.628	6e-78
255560914	2256	RNA binding protein, putative [Ricinus c	0.506	0.070	0.822	4e-76
356513961	2304	PREDICTED: nuclear pore membrane glycopr	0.939	0.128	0.598	2e-73
356558851	372	PREDICTED: RNA-binding protein Musashi h	0.678	0.572	0.704	5e-72
296087606	281	unnamed protein product [Vitis vinifera]	0.605	0.676	0.722	8e-71
363807276	377	uncharacterized protein LOC100793209 [Gl	0.767	0.639	0.661	4e-70
449533873	270	PREDICTED: nuclear polyadenylated RNA-bi	0.732	0.851	0.693	1e-69

>gi|388500070|gb|AFK38101.1| unknown [Lotus japonicus] gi|388508218|gb|AFK42175.1| unknown [Lotus japonicus]

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 213/317 (67%), Positives = 244/317 (76%), Gaps = 23/317 (7%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           MKDRKT QPRGFGF+TYADPSVVDKVIEDTHIINGKQVEIKRTIP+GAVGSKDFKTKKIF
Sbjct: 77  MKDRKTAQPRGFGFITYADPSVVDKVIEDTHIINGKQVEIKRTIPRGAVGSKDFKTKKIF 136

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGGIPS+V EDEF+DFF ++G+V+++QIMRDHST+RSRGFGFITFD+E AVDDLL+ GNK
Sbjct: 137 VGGIPSNVTEDEFRDFFTRYGEVKDNQIMRDHSTNRSRGFGFITFDSEDAVDDLLSMGNK 196

Query: 121 LELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSG 180
           ++ AG QVE+KKAEPKKPN P PS +RYN+ + +Y SG+G+AY             G  G
Sbjct: 197 IDFAGTQVEIKKAEPKKPNPPTPSSKRYNDSRSSYSSGYGEAYD------------GFGG 244

Query: 181 GGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-F 239
             G  GGYRSS AY  R G YGGY  G EFGGYGGY G MG YRG+P SLG++GRYGG F
Sbjct: 245 SYGAAGGYRSSAAYAGRSGAYGGY--GSEFGGYGGYAGAMGPYRGDP-SLGFAGRYGGSF 301

Query: 240 NRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPS--GYDIGLGSSYGGSSGGAFFGSR 297
           +RGYD+ G YGG +ESYG YG     GGG    G    GYD  L   YGG+SGG+F+GSR
Sbjct: 302 SRGYDLGG-YGGASESYGAYGAGAAAGGGSSAAGAYQGGYDASLAGGYGGASGGSFYGSR 360

Query: 298 GGYGGAGGSSRYHPYGR 314
           GGYG      RYHPYGR
Sbjct: 361 GGYGAG----RYHPYGR 373

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488807|ref|XP_002272790.2| PREDICTED: nuclear pore membrane glycoprotein 210-like [Vitis vinifera]

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 180/262 (68%), Positives = 204/262 (77%), Gaps = 20/262 (7%)

Query: 1    MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
            MKDRKTGQPRGFGFVTYAD SVVD+VI+DTH+INGKQVEIKRTIPKGA+G+KDFKTKKIF
Sbjct: 2060 MKDRKTGQPRGFGFVTYADLSVVDQVIQDTHVINGKQVEIKRTIPKGAIGAKDFKTKKIF 2119

Query: 61   VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
            VGGIP++V E+EFKDFF Q+G+V++HQIMRDHSTSRSRGFGF+TFDTEQAVDDLL++GNK
Sbjct: 2120 VGGIPATVTEEEFKDFFTQYGEVKDHQIMRDHSTSRSRGFGFVTFDTEQAVDDLLSQGNK 2179

Query: 121  LELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSG 180
            LELAGAQVE+KKAEPKKPN P P  RRY++ +P +G GFGDAY             G  G
Sbjct: 2180 LELAGAQVEIKKAEPKKPNPPVPPSRRYSDSRPGFGGGFGDAYA------------GFGG 2227

Query: 181  GGGGGGGYRSSGAYGVRGGGYG-------GYGVGGEFGGYGGYGGGMGAYRGEPSSLGYS 233
               G G YRS GAYG R   Y        G   G   GG  G GGG+G YRGEP SLGYS
Sbjct: 2228 SSFGNGPYRSGGAYGSRASAYAGYGGSEFGGYGGYGGGGSSGGGGGIGTYRGEPPSLGYS 2287

Query: 234  GRYGG-FNRGYDVTGDYGGLNE 254
            GRYGG FNRGYD+ G +GG +E
Sbjct: 2288 GRYGGSFNRGYDLGGSHGGPSE 2309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446702|ref|XP_004141110.1| PREDICTED: LOW QUALITY PROTEIN: nuclear pore membrane glycoprotein 210-like [Cucumis sativus]

 Score =  303 bits (776), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 201/322 (62%), Positives = 230/322 (71%), Gaps = 25/322 (7%)

Query: 1    MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
            MKDRKTG PRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKG+  S+DFKTKKIF
Sbjct: 1953 MKDRKTGHPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGSSSSRDFKTKKIF 2012

Query: 61   VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
            VGGIP+SV+EDEF+DFFMQ+G V+EHQIMRDHSTSRSRGFGFITF+TEQAVDDLLA GN+
Sbjct: 2013 VGGIPTSVDEDEFRDFFMQYGVVKEHQIMRDHSTSRSRGFGFITFETEQAVDDLLANGNR 2072

Query: 121  LELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSG 180
            LE+AG+QVE+KKAEPKK N P    +R+++ +P+Y   +GDAY             G  G
Sbjct: 2073 LEMAGSQVEIKKAEPKKANPPPAPSKRFHDSRPSYSGAYGDAY-------------GEFG 2119

Query: 181  GGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-F 239
            GGG GG +R+ G YG RGGGYGGYG     G      GGMGAYR +P S+GYS RYG  F
Sbjct: 2120 GGGYGGSFRAGGPYGARGGGYGGYGGNDFSGYGMYGTGGMGAYREDP-SMGYSARYGASF 2178

Query: 240  NRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGG-------SSGGA 292
            +RGYD  G YGG +ESYG Y   G    GGY G    YD+G+G+ Y          S G 
Sbjct: 2179 SRGYDFRGGYGGPDESYGAYNSGGAPSTGGYAG---SYDMGMGTGYAAGGRGSFYGSRGG 2235

Query: 293  FFGSRGGYGGAGGSSRYHPYGR 314
              G      G+  S RYHPYGR
Sbjct: 2236 GGGGGYDGAGSAPSGRYHPYGR 2257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571134|ref|XP_003553735.1| PREDICTED: heterogeneous nuclear ribonucleoprotein A2 homolog 2-like [Glycine max]

 Score =  296 bits (759), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 200/318 (62%), Positives = 230/318 (72%), Gaps = 23/318 (7%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGS--KDFKTKK 58
           MKDRKTGQPRGFGF+TYADPSVVD VIEDTHIINGKQVEIKRTIP+GA GS  KDF+TKK
Sbjct: 76  MKDRKTGQPRGFGFITYADPSVVDTVIEDTHIINGKQVEIKRTIPRGAAGSNSKDFRTKK 135

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFVGGIPS+V EDEF+DFF ++G+V++HQIMRDHST+RSRGFGFIT+D+E+AVDDLL+ G
Sbjct: 136 IFVGGIPSTVTEDEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITYDSEEAVDDLLSVG 195

Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGG 178
           NK+E AGAQVE+KKAEPKKPN P PS +RYN+ + +YG G              G G+ G
Sbjct: 196 NKIEFAGAQVEIKKAEPKKPNPPAPSSKRYNDSRSSYGGG-------------YGDGYDG 242

Query: 179 SGGGGGGGGYRSSGAYGVRG--GGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRY 236
            GG  G GGYRS GAYG RG  G YGG+  G EFGGYGGY   MG YRG+PS        
Sbjct: 243 FGGNFGMGGYRSGGAYGGRGSAGAYGGF--GSEFGGYGGYASAMGPYRGDPSLGYAGRYG 300

Query: 237 GGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGS 296
           GG+ RG       G    S G     GVGGG       S YD  LG  YGG +GG+F+G+
Sbjct: 301 GGYGRG---YDLGGYGGPSDGYGAYGGVGGGSSGSAYGSSYDASLGGGYGGPAGGSFYGT 357

Query: 297 RGGYGGAGGSSRYHPYGR 314
           RGGY GA G+ RYHPYGR
Sbjct: 358 RGGYAGA-GTGRYHPYGR 374

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255560914|ref|XP_002521470.1| RNA binding protein, putative [Ricinus communis] gi|223539369|gb|EEF40960.1| RNA binding protein, putative [Ricinus communis]

 Score =  291 bits (744), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 134/163 (82%), Positives = 151/163 (92%), Gaps = 4/163 (2%)

Query: 1    MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
            MKDRKTGQPRGFGFVTYADPSVVD+VI+D+H+INGKQVEIKRTIPKGA+G++DFKTKKIF
Sbjct: 1959 MKDRKTGQPRGFGFVTYADPSVVDQVIQDSHVINGKQVEIKRTIPKGAIGARDFKTKKIF 2018

Query: 61   VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
            VGGIP++V E EFK+FFMQ+G+V EHQIMRDHST+RSRGFGFITFDTEQAVDDLLAKGNK
Sbjct: 2019 VGGIPTTVTEVEFKEFFMQYGEVIEHQIMRDHSTNRSRGFGFITFDTEQAVDDLLAKGNK 2078

Query: 121  LELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAY 163
            LELAG QVE+KKAEPKKPN P PS +RYN+ +P    GFGDAY
Sbjct: 2079 LELAGGQVEIKKAEPKKPNPPLPSSKRYNDSRP----GFGDAY 2117

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513961|ref|XP_003525676.1| PREDICTED: nuclear pore membrane glycoprotein 210-like [Glycine max]

 Score =  281 bits (720), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 189/316 (59%), Positives = 222/316 (70%), Gaps = 21/316 (6%)

Query: 1    MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
            MKDRKTGQPRGFGF+TYADPSVVDKVIED HIINGKQVEIKRTIP+GAVGSKDF+TKKIF
Sbjct: 2008 MKDRKTGQPRGFGFITYADPSVVDKVIEDPHIINGKQVEIKRTIPRGAVGSKDFRTKKIF 2067

Query: 61   VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
            VGGIPS+V EDEF+DFF ++G+V++HQIMRDHST+RSRGFGFITFD+E+AVDDLL+ GNK
Sbjct: 2068 VGGIPSNVTEDEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITFDSEEAVDDLLSMGNK 2127

Query: 121  LELAGAQVEVKKAEPKKPNLPQPSYRRYNN-PKPAYGSGFGDAYGGYGGGGFAGGGFGGS 179
            ++ AG+QVE+KKAEPKKP+   PS +R+N+        G+GD Y G+GG    GGG+   
Sbjct: 2128 IDFAGSQVEIKKAEPKKPSSAPPSSKRHNDSRSSYSSGGYGDTYDGFGGSFGMGGGYRSG 2187

Query: 180  GGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG- 238
            G  GGG G    G     G GYGGY   GE G           YRG+  SLGY+GRYGG 
Sbjct: 2188 GAYGGGRGGAYGGFGSEFG-GYGGY--AGEMG----------PYRGD-LSLGYAGRYGGN 2233

Query: 239  FNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRG 298
            F+RGYD+ G YGG +E+YG YG  G   GGG            G   G S G  +  SR 
Sbjct: 2234 FSRGYDL-GGYGGPSENYGAYGAGGGSSGGGGAYQSGYDGNLGGGYGGASGGPFYGSSRA 2292

Query: 299  GYGGAGGSSRYHPYGR 314
            GY     + RYHPYGR
Sbjct: 2293 GY----SAGRYHPYGR 2304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558851|ref|XP_003547716.1| PREDICTED: RNA-binding protein Musashi homolog Rbp6-like [Glycine max]

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 162/230 (70%), Positives = 186/230 (80%), Gaps = 17/230 (7%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVG--SKDFKTKK 58
           MKDRKTGQPRGFGF+TYADPSVVD VIEDTHIINGKQVEIKRTIP+GAVG  SKDF+TKK
Sbjct: 74  MKDRKTGQPRGFGFITYADPSVVDTVIEDTHIINGKQVEIKRTIPRGAVGSNSKDFRTKK 133

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFVGGIPS+V EDEF+DFF ++G+V++HQIMRDHST+RSRGFGFIT+D+E+AVDDLL+ G
Sbjct: 134 IFVGGIPSTVTEDEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITYDSEEAVDDLLSVG 193

Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGG 178
           NK+E AGAQVE+KKAEPKKPN P PS +RYN+ + +YG G              G  + G
Sbjct: 194 NKIEFAGAQVEIKKAEPKKPNPPAPSSKRYNDSRSSYGGG-------------YGDAYDG 240

Query: 179 SGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPS 228
            GG  G GGYRS GAYG RG  YGG+  G EFGGYGGY G MG YRG+PS
Sbjct: 241 FGGNFGMGGYRSGGAYGGRGSAYGGF--GSEFGGYGGYAGAMGPYRGDPS 288

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087606|emb|CBI34862.3| unnamed protein product [Vitis vinifera]

 Score =  273 bits (698), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 146/202 (72%), Positives = 166/202 (82%), Gaps = 12/202 (5%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           MKDRKTGQPRGFGFVTYAD SVVD+VI+DTH+INGKQVEIKRTIPKGA+G+KDFKTKKIF
Sbjct: 73  MKDRKTGQPRGFGFVTYADLSVVDQVIQDTHVINGKQVEIKRTIPKGAIGAKDFKTKKIF 132

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGGIP++V E+EFKDFF Q+G+V++HQIMRDHSTSRSRGFGF+TFDTEQAVDDLL++GNK
Sbjct: 133 VGGIPATVTEEEFKDFFTQYGEVKDHQIMRDHSTSRSRGFGFVTFDTEQAVDDLLSQGNK 192

Query: 121 LELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSG 180
           LELAGAQVE+KKAEPKKPN P P  RRY++ +P +G GFGDAY             G  G
Sbjct: 193 LELAGAQVEIKKAEPKKPNPPVPPSRRYSDSRPGFGGGFGDAYA------------GFGG 240

Query: 181 GGGGGGGYRSSGAYGVRGGGYG 202
              G G YRS GAYG R   Y 
Sbjct: 241 SSFGNGPYRSGGAYGSRASAYA 262

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807276|ref|NP_001242362.1| uncharacterized protein LOC100793209 [Glycine max] gi|255636483|gb|ACU18580.1| unknown [Glycine max]

 Score =  270 bits (691), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 170/257 (66%), Positives = 203/257 (78%), Gaps = 16/257 (6%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           MKDRKTGQPRGFGF+TYADPSVVDKVIE+ H+INGKQVEIKRTIP+GAVGSKDF+TKKIF
Sbjct: 74  MKDRKTGQPRGFGFITYADPSVVDKVIEEPHVINGKQVEIKRTIPRGAVGSKDFRTKKIF 133

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGGIPS+V EDEF+DFF ++G+V++HQIMRDHST+RSRGFGFITF++E+AVDDLL+ GNK
Sbjct: 134 VGGIPSNVTEDEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITFESEEAVDDLLSMGNK 193

Query: 121 LELAGAQVEVKKAEPKKPNLPQPSYRRYNN-PKPAYGSGFGDAYGGYGGGGFAGGGFGGS 179
           ++ AGAQVE+KKAEPKKPN   PS +RYN+        G+GDAY G+GG    GGG+   
Sbjct: 194 IDFAGAQVEIKKAEPKKPNSAPPSSKRYNDSRSSYSSGGYGDAYDGFGGSFGMGGGYRSG 253

Query: 180 GGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG- 238
           G  GGG G  + G +              EFGGYGGY G MG YRG+P SLGY+GRYGG 
Sbjct: 254 GAYGGGRGSGAYGGH------------ASEFGGYGGYAGAMGPYRGDP-SLGYAGRYGGS 300

Query: 239 FNRGYDVTGDYGGLNES 255
           F+RGYD+ G YGG +E+
Sbjct: 301 FSRGYDLGG-YGGPSEN 316

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449533873|ref|XP_004173895.1| PREDICTED: nuclear polyadenylated RNA-binding protein 4-like, partial [Cucumis sativus]

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 170/245 (69%), Positives = 194/245 (79%), Gaps = 15/245 (6%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           MKDRKTG PRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKG+  S+DFKTKKIF
Sbjct: 38  MKDRKTGHPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGSSSSRDFKTKKIF 97

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGGIP+SV+EDEF+DFFMQ+G V+EHQIMRDHSTSRSRGFGFITF+TEQAVDDLLA GN+
Sbjct: 98  VGGIPTSVDEDEFRDFFMQYGVVKEHQIMRDHSTSRSRGFGFITFETEQAVDDLLANGNR 157

Query: 121 LELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSG 180
           LE+AG+QVE+KKAEPKK N P    +R+++ +P+Y   +GDAY             G  G
Sbjct: 158 LEMAGSQVEIKKAEPKKANPPPAPSKRFHDSRPSYSGAYGDAY-------------GEFG 204

Query: 181 GGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-F 239
           GGG GG +R+ G YG RGGGYGGYG     G      GGMGAYR +P S+GYS RYG  F
Sbjct: 205 GGGYGGSFRAGGPYGARGGGYGGYGGNDFSGYGMYGTGGMGAYREDP-SMGYSARYGASF 263

Query: 240 NRGYD 244
           +RGYD
Sbjct: 264 SRGYD 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	314
TAIR|locus:2168848	423	AT5G40490 [Arabidopsis thalian	0.464	0.345	0.775	2.8e-67
TAIR|locus:504955752	358	AT3G13224 [Arabidopsis thalian	0.461	0.405	0.729	4.2e-59
TAIR|locus:2007903	369	AT1G17640 [Arabidopsis thalian	0.464	0.395	0.526	1.7e-40
TAIR|locus:2133862	455	AT4G26650 [Arabidopsis thalian	0.283	0.195	0.544	3.1e-36
TAIR|locus:2173967	460	AT5G55550 [Arabidopsis thalian	0.433	0.295	0.483	1.9e-33
TAIR|locus:2129590	411	AT4G14300 [Arabidopsis thalian	0.439	0.335	0.438	8.8e-32
TAIR|locus:2077392	495	AT3G07810 [Arabidopsis thalian	0.449	0.284	0.471	2.1e-30
TAIR|locus:2050992	404	AT2G33410 [Arabidopsis thalian	0.439	0.341	0.445	2.7e-29
ASPGD|ASPL0000063757	559	AN10941 [Emericella nidulans (	0.414	0.232	0.470	2.6e-28
CGD|CAL0003460	475	orf19.5989 [Candida albicans (	0.414	0.273	0.474	5e-27

TAIR|locus:2168848 AT5G40490 [Arabidopsis thaliana (taxid:3702)]

 Score = 609 (219.4 bits), Expect = 2.8e-67, Sum P(3) = 2.8e-67
 Identities = 114/147 (77%), Positives = 133/147 (90%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
             MKDRKTGQPRGFGFVTYAD SVVDKVI+D HII GKQVEIKRTIP+G++ S DFKTKKIF
Sbjct:    74 MKDRKTGQPRGFGFVTYADSSVVDKVIQDNHIIIGKQVEIKRTIPRGSMSSNDFKTKKIF 133

Query:    61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
             VGGIPSSV++DEFK+FFMQFG+++EHQIMRDHST RSRGFGF+T+++E  VD LLAKGN+
Sbjct:   134 VGGIPSSVDDDEFKEFFMQFGELKEHQIMRDHSTGRSRGFGFVTYESEDMVDHLLAKGNR 193

Query:   121 LELAGAQVEVKKAEPKKPN-LPQPSYR 146
             +EL+G QVE+KKAEPKKPN +  PS R
Sbjct:   194 IELSGTQVEIKKAEPKKPNSVTTPSKR 220

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=IDA

TAIR|locus:504955752 AT3G13224 [Arabidopsis thaliana (taxid:3702)]

 Score = 575 (207.5 bits), Expect = 4.2e-59, Sum P(2) = 4.2e-59
 Identities = 108/148 (72%), Positives = 128/148 (86%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVG--SKDFKTKK 58
             M+DR TGQPRGFGF+T+ADPSVVDKVIEDTH+INGKQVEIKRTIPKGA G  SKD KTKK
Sbjct:    51 MRDRHTGQPRGFGFITFADPSVVDKVIEDTHVINGKQVEIKRTIPKGAGGNQSKDIKTKK 110

Query:    59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
             IFVGGIPS+V EDE KDFF ++G+V EHQ++RDH T+RSRGFGF+ FD+E+ VD+LL+KG
Sbjct:   111 IFVGGIPSTVTEDELKDFFAKYGNVVEHQVIRDHETNRSRGFGFVIFDSEEVVDELLSKG 170

Query:   119 NKLELAGAQVEVKKAEPKKP-NLPQPSY 145
             N +++A  QVE+KKAEPKK  N   PSY
Sbjct:   171 NMIDMADTQVEIKKAEPKKSLNRSPPSY 198

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2007903 AT1G17640 [Arabidopsis thaliana (taxid:3702)]

 Score = 411 (149.7 bits), Expect = 1.7e-40, Sum P(2) = 1.7e-40
 Identities = 80/152 (52%), Positives = 108/152 (71%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFK----T 56
             M DR TG PRGFGFVT+AD +V +KV+E+ H+I+ ++V++KRT+P+G   + D K    T
Sbjct:    98 MTDRITGNPRGFGFVTFADSAVAEKVLEEDHVIDDRKVDLKRTLPRGDKDT-DIKAVSKT 156

Query:    57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
             +KIFVGG+P  + EDE K++F  +GD+ EHQIM DH T RSRGFGF+TF TE +VD L +
Sbjct:   157 RKIFVGGLPPLLEEDELKNYFCVYGDIIEHQIMYDHHTGRSRGFGFVTFQTEDSVDRLFS 216

Query:   117 KGNKLELAGAQVEVKKAEPKKPNLPQPSYRRY 148
              G   EL   QVE+K+AEPK+      S+R Y
Sbjct:   217 DGKVHELGDKQVEIKRAEPKRTGRDN-SFRSY 247

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2133862 AT4G26650 [Arabidopsis thaliana (taxid:3702)]

 Score = 242 (90.2 bits), Expect = 3.1e-36, Sum P(3) = 3.1e-36
 Identities = 49/90 (54%), Positives = 66/90 (73%)

Query:    55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
             +TKKIFVGG+PSS+ E EFK++F QFG + +  +M DH+T R RGFGFITFD+E++VD +
Sbjct:   120 RTKKIFVGGLPSSITEAEFKNYFDQFGTIADVVVMYDHNTQRPRGFGFITFDSEESVDMV 179

Query:   115 LAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
             L K    EL G  VEVK+A PK+ +   P+
Sbjct:   180 LHKTFH-ELNGKMVEVKRAVPKELSSTTPN 208

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0042732 "D-xylose metabolic process" evidence=RCA

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

 Score = 344 (126.2 bits), Expect = 1.9e-33, Sum P(2) = 1.9e-33
 Identities = 74/153 (48%), Positives = 100/153 (65%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK-------------- 46
             M+DR TG+ RGFGF+ +ADP V ++VI D HII+G+ VE K+ +P+              
Sbjct:    38 MRDRATGRARGFGFIVFADPCVSERVIMDKHIIDGRTVEAKKAVPRDDQQVLKRHASPIH 97

Query:    47 --GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
                 V     +TKKIFVGG+PSS+ E+EFK++F QFG + +  +M DH+T R RGFGFIT
Sbjct:    98 LMSPVHGGGGRTKKIFVGGLPSSITEEEFKNYFDQFGTIADVVVMYDHNTQRPRGFGFIT 157

Query:   105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 137
             FD++ AVD +L K    EL G  VEVK+A PK+
Sbjct:   158 FDSDDAVDRVLHKTFH-ELNGKLVEVKRAVPKE 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

 Score = 327 (120.2 bits), Expect = 8.8e-32, Sum P(2) = 8.8e-32
 Identities = 68/155 (43%), Positives = 105/155 (67%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK------GAVGSKDF 54
             M+D+ TG+PRGFGFV ++DPSV+D+V+++ H I+ ++V++KR + +      G  G+ + 
Sbjct:    38 MRDKLTGRPRGFGFVIFSDPSVLDRVLQEKHSIDTREVDVKRAMSREEQQVSGRTGNLNT 97

Query:    55 ----------KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
                       KTKKIFVGG+P ++ ++EF+ +F  +G V +  IM D +T+R RGFGF++
Sbjct:    98 SRSSGGDAYNKTKKIFVGGLPPTLTDEEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVS 157

Query:   105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
             FD+E AVD +L K    +L+G QVEVK+A PK  N
Sbjct:   158 FDSEDAVDSVLHKTFH-DLSGKQVEVKRALPKDAN 191

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

TAIR|locus:2077392 AT3G07810 [Arabidopsis thaliana (taxid:3702)]

 Score = 336 (123.3 bits), Expect = 2.1e-30, P = 2.1e-30
 Identities = 75/159 (47%), Positives = 103/159 (64%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK-------------- 46
             +KDR TG+ RGFGFV +ADP+V + VI + H I+G+ VE K+ +P+              
Sbjct:    38 LKDRTTGRARGFGFVVFADPAVAEIVITEKHNIDGRLVEAKKAVPRDDQNMVNRSNSSSI 97

Query:    47 -GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
              G+ G    +T+KIFVGG+PSSV E +FK +F QFG   +  +M DH+T R RGFGFIT+
Sbjct:    98 QGSPGGPG-RTRKIFVGGLPSSVTESDFKTYFEQFGTTTDVVVMYDHNTQRPRGFGFITY 156

Query:   106 DTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
             D+E+AV+ +L K    EL G  VEVK+A PK+ + P PS
Sbjct:   157 DSEEAVEKVLLKTFH-ELNGKMVEVKRAVPKELS-PGPS 193

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005576 "extracellular region" evidence=ISM

TAIR|locus:2050992 AT2G33410 [Arabidopsis thaliana (taxid:3702)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 69/155 (44%), Positives = 103/155 (66%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI------PKGAVG---- 50
             M+++ TG+PRGFGFV ++DP+V+D+V++D H I+ + V++KR +      P G  G    
Sbjct:    38 MREKATGRPRGFGFVAFSDPAVIDRVLQDKHHIDNRDVDVKRAMSREEQSPAGRSGTFNA 97

Query:    51 SKDF------KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
             S++F      +TKKIFVGG+P ++  DEF+ +F  +G V +  IM D +T R RGFGF++
Sbjct:    98 SRNFDSGANVRTKKIFVGGLPPALTSDEFRAYFETYGPVSDAVIMIDQTTQRPRGFGFVS 157

Query:   105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
             FD+E +VD +L K    +L G QVEVK+A PK  N
Sbjct:   158 FDSEDSVDLVLHKTFH-DLNGKQVEVKRALPKDAN 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 321 (118.1 bits), Expect = 2.6e-28, P = 2.6e-28
 Identities = 64/136 (47%), Positives = 89/136 (65%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
             M+D  TG+ RGFGF+T+ DP  V+ V+   H ++GK ++ KR IP+     +  KT KIF
Sbjct:   142 MRDSATGRSRGFGFLTFKDPKTVNTVMVKEHYLDGKIIDPKRAIPR----DEQEKTSKIF 197

Query:    61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
             VGG+     E +FK FFMQFG V +  +M D  T R RGFGF+TFD+E AV+  L++   
Sbjct:   198 VGGVSQEATEQDFKQFFMQFGRVIDATLMIDKDTGRPRGFGFVTFDSEAAVEAALSR--P 255

Query:   121 LELAGAQVEVKKAEPK 136
             LE+ G  +EVKKA+P+
Sbjct:   256 LEILGKTIEVKKAQPR 271

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

CGD|CAL0003460 orf19.5989 [Candida albicans (taxid:5476)]

 Score = 306 (112.8 bits), Expect = 5.0e-27, P = 5.0e-27
 Identities = 65/137 (47%), Positives = 88/137 (64%)

Query:     1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
             MKD  TG+ RGFGF+T+ D   VD +++D H+++GK ++ KR I K        K  KIF
Sbjct:   194 MKDSATGRSRGFGFLTFEDAKSVDALLKDRHVLDGKLIDPKRAISK----EDQEKVGKIF 249

Query:    61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
             VGGI   V E+EF +FF QFG + + Q+M D  T RSRGFGF+T+D+  AVD +    NK
Sbjct:   250 VGGIDPMVTEEEFDNFFSQFGKIIDCQLMIDKDTGRSRGFGFVTYDSPAAVDKVCV--NK 307

Query:   121 -LELAGAQVEVKKAEPK 136
              L L G  +EVK+A P+
Sbjct:   308 YLTLKGKAMEVKRAAPR 324

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005849 "mRNA cleavage factor complex" evidence=IEA

GO:0006379 "mRNA cleavage" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	314
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-30
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-27
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-20
smart00360	73	smart00360, RRM, RNA recognition motif	2e-19
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-18
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-16
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	9e-16
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-15
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-15
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-15
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-14
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-14
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-14
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-14
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	6e-14
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-13
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-13
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-13
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-13
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-13
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-13
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-13
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-13
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-12
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-12
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-12
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-12
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	5e-12
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	7e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-12
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-12
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	9e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	9e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-12
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	5e-11
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	8e-11
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-10
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-10
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	1e-10
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-10
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-10
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-10
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-10
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	3e-10
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-10
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	5e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-10
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	9e-10
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	1e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-09
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	3e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-09
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-09
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-09
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-09
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-09
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-08
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-08
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-08
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	4e-08
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-08
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	5e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	7e-08
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	7e-08
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	7e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-08
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	9e-08
smart00360	73	smart00360, RRM, RNA recognition motif	1e-07
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-07
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-07
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-07
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	2e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-07
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-07
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	4e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	7e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	9e-07
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-06
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-06
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	4e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	4e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-06
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-06
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	6e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-06
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	8e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	8e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	8e-06
cd12410	93	cd12410, RRM2_RRT5, RNA recognition motif 2 in yea	9e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-05
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	1e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	2e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	4e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	4e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-05
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	4e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	4e-05
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	4e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	6e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	6e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	9e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	1e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-04
cd12444	112	cd12444, RRM1_CPEBs, RNA recognition motif 1 in cy	2e-04
cd12753	85	cd12753, RRM1_RBM10, RNA recognition motif 1 in ve	2e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-04
PRK14279	392	PRK14279, PRK14279, chaperone protein DnaJ; Provis	3e-04
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-04
pfam11456	102	pfam11456, DUF3019, Protein of unknown function (D	4e-04
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	4e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-04
PRK07772	186	PRK07772, PRK07772, single-stranded DNA-binding pr	4e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	5e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-04
PLN03138	796	PLN03138, PLN03138, Protein TOC75; Provisional	5e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	5e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	6e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	6e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	6e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	8e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	8e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	8e-04
cd12624	91	cd12624, RRM_PRC, RNA recognition motif in peroxis	8e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	8e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	9e-04
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	0.001
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.001
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.001
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.001
pfam07466	280	pfam07466, DUF1517, Protein of unknown function (D	0.001
cd12295	74	cd12295, RRM_YRA2, RNA recognition motif in yeast	0.001
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.001
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	0.001
COG4371	334	COG4371, COG4371, Predicted membrane protein [Func	0.001
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.001
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.001
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.001
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	0.001
pfam12810	248	pfam12810, Gly_rich, Glycine rich protein	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.002
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.002
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
PRK06958	182	PRK06958, PRK06958, single-stranded DNA-binding pr	0.002
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.002
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	0.002
PRK07772	186	PRK07772, PRK07772, single-stranded DNA-binding pr	0.003
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	0.003
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.003
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.003
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.003
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.003
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.004
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.004
PRK07772	186	PRK07772, PRK07772, single-stranded DNA-binding pr	0.004
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.004
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.004
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.004
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.004

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

 Score =  110 bits (276), Expect = 1e-30
 Identities = 40/81 (49%), Positives = 57/81 (70%), Gaps = 1/81 (1%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           +TKKIFVGG+P +V E + + +F QFG V E  +M DH   R RGFGFITF++E +VD +
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 115 LAKGNKLELAGAQVEVKKAEP 135
           + +    ++ G +VEVK+AEP
Sbjct: 61  VNEHFH-DINGKKVEVKRAEP 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score =  102 bits (255), Expect = 1e-27
 Identities = 46/76 (60%), Positives = 59/76 (77%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+P  V E+EFK++F QFG V + Q+M+DH T RSRGFGF+TFD+E AV+ + + 
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 118 GNKLELAGAQVEVKKA 133
           G  LEL G QVEVK+A
Sbjct: 61  G-MLELGGKQVEVKRA 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 = 81.6 bits (202), Expect = 6e-20
 Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+     E++ +++F +FG++ E ++  D  T++ RGF FITFD+E+ V  +L +
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKIL-E 59

Query: 118 GNKLELAGAQVEVKKA 133
                + G +VEVKKA
Sbjct: 60  TQFHVIGGKKVEVKKA 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|214636 smart00360, RRM, RNA recognition motif

 Score = 80.3 bits (199), Expect = 2e-19
 Identities = 25/73 (34%), Positives = 44/73 (60%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            +FVG +P    E+E ++ F +FG V+  +++RD  T +S+GF F+ F++E+  +  L  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 118 GNKLELAGAQVEV 130
            N  EL G  ++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 77.1 bits (190), Expect = 4e-18
 Identities = 33/75 (44%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+ ++  ED+ K +F QFG V++  +M D  T+R RGFGF+TF++E  VD  + +
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDK-VCE 59

Query: 118 GNKLELAGAQVEVKK 132
            +  E+    VE KK
Sbjct: 60  IHFHEINNKMVECKK 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 75.7 bits (187), Expect = 1e-17
 Identities = 28/78 (35%), Positives = 46/78 (58%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            ++VG +P +V E++ KD F QFG+V   +++ D  T RSRGFGF+  +T +  +  + K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 118 GNKLELAGAQVEVKKAEP 135
            N  +  G  + V +A P
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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|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 = 73.4 bits (181), Expect = 1e-16
 Identities = 30/76 (39%), Positives = 46/76 (60%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FV G+ +   E E +  F +FG V+E  +M+D  T  SRGFGF+TF++ +  D  +  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 118 GNKLELAGAQVEVKKA 133
            N  EL G  ++V+KA
Sbjct: 63  LNGKELEGRVIKVEKA 78

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

 Score = 78.1 bits (191), Expect = 2e-16
 Identities = 35/147 (23%), Positives = 67/147 (45%), Gaps = 5/147 (3%)

Query: 18  ADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKK-----IFVGGIPSSVNEDE 72
                  ++ E      G   E +  + + +   K  +  K     +FVG +P  V E++
Sbjct: 72  RKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEED 131

Query: 73  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 132
            ++ F +FG V+  +++RD  T +SRGF F+ F++E++ +  + + N  EL G  + V+K
Sbjct: 132 LRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQK 191

Query: 133 AEPKKPNLPQPSYRRYNNPKPAYGSGF 159
           A+P      + S     +       G 
Sbjct: 192 AQPASQPRSELSNNLDASFAKKLSRGK 218

Length = 306

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

 Score = 71.6 bits (176), Expect = 4e-16
 Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +P    E++ ++ F +FG+++  +I+RD    +S+GF F+ F++ +  +  L   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 119 NKLELAGAQVEVK 131
           N  EL G +++V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 70.3 bits (173), Expect = 9e-16
 Identities = 23/42 (54%), Positives = 33/42 (78%), Gaps = 1/42 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 41
          MKD  TG+ RGFGFVT+ADPS VDKV+    H+++G++++ K
Sbjct: 31 MKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGREIDPK 72

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

 Score = 69.6 bits (171), Expect = 3e-15
 Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 2/76 (2%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +IFVGGIP    E+E +DFF +FG V++ +I+ D     S+G+GF+TF+T++  + +LA 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 118 GNKLELAGAQVEVKKA 133
           GN L   G ++ +  A
Sbjct: 63  GN-LNFRGKKLNIGPA 77

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|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 = 4e-15
 Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+GG+     E+  +++F ++G+V +  IM+D  T RSRGFGF+TF    +VD +LA  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 119 NKLELAGAQVEVK 131
             + L G +++ K
Sbjct: 61  PHV-LDGREIDPK 72

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

 Score = 74.9 bits (184), Expect = 5e-15
 Identities = 53/223 (23%), Positives = 82/223 (36%), Gaps = 23/223 (10%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--------IINGKQVEIKRTIPKGAVGSK 52
           +KDR + + +G  +V + D   V K +  T         I+   Q E  R          
Sbjct: 122 IKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPG 181

Query: 53  DFKT-KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQA 110
           D     K++VG +  ++ E E +  F  FGD+++ Q+ RD  T RS+GFGFI F D E+A
Sbjct: 182 DIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEA 241

Query: 111 VDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGG 170
            + L    N  ELAG  ++V  A+     L         +    +         G     
Sbjct: 242 KEALEVM-NGFELAGRPIKVGYAQDSTYLL---------DAANTFEDIDKQQQMGKNLNT 291

Query: 171 FAGGGF---GGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEF 210
                         G GG     +G+           G+    
Sbjct: 292 EEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPN 334

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 67.2 bits (165), Expect = 1e-14
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++V  +P SV E++ ++FF  +G V+  +++R+    R RGF F+ F + +  +  L K 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 119 NKLELAGAQVE 129
           N L L G  + 
Sbjct: 59  NGLVLDGRTLR 69

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

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

 Score = 67.1 bits (164), Expect = 2e-14
 Identities = 30/75 (40%), Positives = 50/75 (66%), Gaps = 1/75 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+GG+      +  +++F +FG+++E  +MRD +T RSRGFGF+TF    +VD +LA+G
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 119 NKLELAGAQVEVKKA 133
              EL G +++ K A
Sbjct: 61  -PHELDGKKIDPKVA 74

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

 Score = 67.0 bits (163), Expect = 2e-14
 Identities = 33/79 (41%), Positives = 52/79 (65%), Gaps = 1/79 (1%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           +TKKIFVGG+ ++   ++ K +F QFG V++  +M D +T+R RGFGF+TF+ E  V+  
Sbjct: 2   RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK- 60

Query: 115 LAKGNKLELAGAQVEVKKA 133
           + + +  E+    VE KKA
Sbjct: 61  VCEIHFHEINNKMVECKKA 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 66.1 bits (162), Expect = 4e-14
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +P    E++ KD F +FG ++  +I+RD  T RS+GF F+ F+ E+  +  L   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 119 NKLELAGAQVE 129
           N  EL G ++ 
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 65.9 bits (161), Expect = 5e-14
 Identities = 31/80 (38%), Positives = 54/80 (67%), Gaps = 3/80 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-A 116
           K+F+GG+     +D  K++F Q+G++ +  +M+D +T RSRGFGF+TF +   VD  + A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 117 KGNKLELAGAQVEVKKAEPK 136
           + +K++  G +VE K+A P+
Sbjct: 61  RPHKVD--GREVEPKRAVPR 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 65.8 bits (160), Expect = 6e-14
 Identities = 30/81 (37%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           KKIFVGGI     E   +D+F ++G ++  ++M D  + + RGF F+TFD    VD ++ 
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60

Query: 117 KGNKLELAGAQVEVKKAEPKK 137
           +     + G   EVKKA  K+
Sbjct: 61  QKYH-TINGHNCEVKKALSKQ 80

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

 Score = 65.1 bits (159), Expect = 1e-13
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++FVG +P  + EDE K+FF +FG+V E +I       R   FGF+ FD  +AV  +LA 
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

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

 Score = 64.6 bits (157), Expect = 1e-13
 Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+     ++  +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 118 GNKLELAGAQVEVKKA 133
            ++ EL    ++ K A
Sbjct: 62  -SRHELDSKTIDPKVA 76

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

 Score = 64.7 bits (158), Expect = 1e-13
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            + V G+P    E + KD+F  FG++   Q+ +D  T +S+GFGF+ F   +    +L++
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 118 GNKLELAGAQVEVKKAEPK 136
            + ++  G   +VK    K
Sbjct: 61  RHMID--GRWCDVKIPNSK 77

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

 Score = 64.5 bits (157), Expect = 1e-13
 Identities = 29/78 (37%), Positives = 53/78 (67%), Gaps = 2/78 (2%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+GG+     +D  +++F QFG+V +  +MRD +T RSRGFGF+TF   ++V++++ K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 119 NKLELAGAQVEVKKAEPK 136
           + L+  G  ++ K+A P+
Sbjct: 61  HILD--GKIIDPKRAIPR 76

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|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 = 64.1 bits (157), Expect = 2e-13
 Identities = 19/55 (34%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAV 111
           K+FVG +P +  E++ +  F ++G+++E  I+RD  T +S+G  F+ F + E+A 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQ 55

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

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ 
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60

Query: 117 KGNKLELAGAQVEVKKA 133
           +     + G   EV+KA
Sbjct: 61  QKYH-TVNGHNCEVRKA 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 62.7 bits (153), Expect = 6e-13
 Identities = 28/74 (37%), Positives = 47/74 (63%), Gaps = 1/74 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVGG+   V E++ +++F Q+G+V+  +I+ D  T + RGF F+TFD    VD ++ +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 118 GNKLELAGAQVEVK 131
                + G +VEVK
Sbjct: 61  KYHT-INGHRVEVK 73

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

 Score = 62.8 bits (152), Expect = 7e-13
 Identities = 27/60 (45%), Positives = 43/60 (71%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+    + D  +D+F +FG+++E  +MRD +T RSRGFGF+TF    +VD +LA+
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

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

 Score = 68.3 bits (167), Expect = 8e-13
 Identities = 44/143 (30%), Positives = 72/143 (50%), Gaps = 18/143 (12%)

Query: 6   TGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPKGA-VGSKDFKTKKIFVG 62
            G+ RG+GFV +         I+  +  ++N K+V + R I K     +   K   ++V 
Sbjct: 125 NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVK 184

Query: 63  GIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ----AVD------ 112
            +  SVNED+ ++ F +FG++    +M+D S  RSRGF F+ F+  +    AV+      
Sbjct: 185 NLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKK 243

Query: 113 -DLLAKGNKLELAGAQVEVKKAE 134
             L  +G KL +  AQ   K+AE
Sbjct: 244 IGLAKEGKKLYVGRAQ---KRAE 263

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

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 7/78 (8%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           +K+FVG +   + E++ + +F QFG+V +  I +       R F F+TF   +    L  
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLC- 54

Query: 117 KGNKLELAGAQVEVKKAE 134
            G    + G  V V  AE
Sbjct: 55  -GEDHIIKGVSVHVSNAE 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 20/78 (25%), Positives = 44/78 (56%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FV  +P    +++ ++FF + G ++   +++D  + + RGFG++TF  E+     L + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 119 NKLELAGAQVEVKKAEPK 136
            K +  G ++ V+ A+ K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 61.0 bits (148), Expect = 3e-12
 Identities = 28/77 (36%), Positives = 48/77 (62%), Gaps = 3/77 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-A 116
           K+FVGG+    ++   +  F ++G + E  +M D +T RSRGFGFITF +    D+ + A
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 117 KGNKLELAGAQVEVKKA 133
           + + ++  G Q+E+K+A
Sbjct: 64  QPHSID--GNQIELKRA 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++VG +  ++ ED+ +  F  FG+++  Q+ RD  T RS+G+GFI F   +     L + 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 119 NKLELAGAQVEV 130
           N  ELAG  ++V
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 60.3 bits (147), Expect = 5e-12
 Identities = 25/57 (43%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVD 112
            KIFVGG+P    +D  + +F QFG+++E  ++ D  T +SRG+GF+TF D E A  
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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 60.4 bits (146), Expect = 5e-12
 Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+  +   ++ K +F QFG V +  +M D +T+R RGFGF+TF++E  V+  + +
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCE 59

Query: 118 GNKLELAGAQVEVKK 132
            +  E+    VE KK
Sbjct: 60  IHFHEINNKMVECKK 74

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

 Score = 60.0 bits (146), Expect = 6e-12
 Identities = 24/76 (31%), Positives = 42/76 (55%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +I+V  +   ++ED+ K  F  FG ++   +  D  T + +G+GFI ++  Q+  D +A 
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 118 GNKLELAGAQVEVKKA 133
            N  +L G Q+ V KA
Sbjct: 62  MNLFDLGGQQLRVGKA 77

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

 Score = 60.2 bits (146), Expect = 7e-12
 Identities = 26/64 (40%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +IFVGGI    NE++ + FF Q+G V+E +I+ D +   S+G+GF+TF+T++    +L +
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62

Query: 118 GNKL 121
            N+L
Sbjct: 63  ANRL 66

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

 Score = 65.0 bits (158), Expect = 7e-12
 Identities = 44/174 (25%), Positives = 71/174 (40%), Gaps = 9/174 (5%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKD-FKTKKI 59
           ++D+ TGQ  G+GFV Y  P   +K +   + +NG +++ K      A  S D  K   +
Sbjct: 36  VRDKVTGQSLGYGFVNYVRPEDAEKAV---NSLNGLRLQNKTIKVSYARPSSDSIKGANL 92

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           +V G+P ++ + E +  F  FG +   +I+ D+ T  S+G GFI FD     D  +   N
Sbjct: 93  YVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN 152

Query: 120 KLELAGA--QVEVKKAE---PKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGG 168
               +G    + VK A                   NP+               G
Sbjct: 153 GTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIG 206

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|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 = 59.9 bits (145), Expect = 7e-12
 Identities = 26/76 (34%), Positives = 42/76 (55%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+    NE   +  F ++G + E  +++D  T RSRGFGF+TF+      D +  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 118 GNKLELAGAQVEVKKA 133
            N   + G Q+ V +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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 59.8 bits (145), Expect = 9e-12
 Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVGG+     ++  + +F Q+G+V +  IM+D +T+RSRGFGF+ F     V  +LA 
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 118 GNKLELAGAQVEVKKAEPK 136
           G    L G  ++ K   P+
Sbjct: 61  GPHT-LDGRTIDPKPCTPR 78

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

 Score = 59.9 bits (145), Expect = 9e-12
 Identities = 23/78 (29%), Positives = 40/78 (51%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FV  +  SV +++  DFF     ++   ++ D  T  SRG+GF+TF   +   + LAK 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 119 NKLELAGAQVEVKKAEPK 136
              +L G  + +  AE +
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

 Score = 59.5 bits (145), Expect = 9e-12
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 8/71 (11%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           ++VGG+   V+E      F+ FGD+++ QI  D+ T + RGF F+ F    D   A+D++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 115 LAKGNKLELAG 125
               N+ EL G
Sbjct: 61  ----NESELFG 67

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

 Score = 57.6 bits (139), Expect = 5e-11
 Identities = 31/81 (38%), Positives = 48/81 (59%), Gaps = 3/81 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD-LLA 116
           K+FVGG+   V E +  + F QFG V++ +++ D  T + RGFGF+ F    + D   + 
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 117 KGNKLELAGAQVEVKKAEPKK 137
           K + +   G +VEVKKA PK+
Sbjct: 61  KFHPIN--GHRVEVKKAVPKE 79

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

 Score = 56.9 bits (137), Expect = 8e-11
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVGG+    ++ + KD+F +FG+V +  I  D +T RSRGFGFI F    +V+ +L +
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 118 GNKLELAGAQVEVKKA 133
             +  L G  ++ KKA
Sbjct: 61  -KEHRLDGRLIDPKKA 75

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

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVG +P +V   E K++F QFG V+   +  D  T  S+G+GF++F +   +++ L K
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 118 GNKLELAGAQVEVK 131
             K  L G +++V+
Sbjct: 61  -QKHILEGNKLQVQ 73

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

 Score = 62.0 bits (150), Expect = 1e-10
 Identities = 38/151 (25%), Positives = 72/151 (47%), Gaps = 9/151 (5%)

Query: 3   DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR--TIPKGA-----VGSKD 53
           D  TG+ +GF FV Y  P      +E  +  ++ G+ +++ R   +P+       V  + 
Sbjct: 142 DPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEA 201

Query: 54  FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
            K  +I+V  +   ++E + K  F  FG++ + Q+ R  +    +G+GFI ++  Q+  +
Sbjct: 202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE 261

Query: 114 LLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
            +A  N  +L G  + V K       L QP+
Sbjct: 262 AIASMNLFDLGGQYLRVGKCVTPPDALLQPA 292

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

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

 Score = 56.5 bits (136), Expect = 1e-10
 Identities = 28/77 (36%), Positives = 48/77 (62%), Gaps = 1/77 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           KKIFVGG+     E++ +++F +FG+++  ++  D  T++ RGF FITF  E  V  +L 
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

Query: 117 KGNKLELAGAQVEVKKA 133
           K     ++G++ E+K A
Sbjct: 65  KKFH-NVSGSKCEIKVA 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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 56.3 bits (135), Expect = 1e-10
 Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 3/80 (3%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD-D 113
           + +K+F+GG+     +D  ++ F ++G + +  +MRD  T RSRGFGF+T+   + VD  
Sbjct: 1   QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

Query: 114 LLAKGNKLELAGAQVEVKKA 133
           + A+ +K++  G  VE K+A
Sbjct: 61  MSARPHKVD--GRVVEPKRA 78

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

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 23/46 (50%), Positives = 31/46 (67%), Gaps = 1/46 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKRTIP 45
          M D +  +PRGFGF+T+     VD+V+ E  H INGK+VE+KR  P
Sbjct: 35 MYDHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGKKVEVKRAEP 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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 21/46 (45%), Positives = 34/46 (73%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 46
          M+D  TG+ RGFGF+T+  P  V++V++  HI++GK ++ KR IP+
Sbjct: 31 MRDSATGRSRGFGFLTFKKPKSVNEVMKKEHILDGKIIDPKRAIPR 76

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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           + +F+  +P    E+E K+ F QFG+V+  +I++D  T  S+G  F+ F T+++    L 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 117 KGNK-----LELAGAQVEVKKA 133
             +      L L G ++ V  A
Sbjct: 61  AADNAEDSGLSLDGRRLIVTLA 82

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

 Score = 55.9 bits (134), Expect = 2e-10
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           +K+F+GG+     E+  ++++ Q+G + +  +MRD ++ RSRGFGF+TF     VD  +A
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 117 KGNKLELAGAQVEVKKA 133
                 + G  VE K+A
Sbjct: 63  -ARPHTIDGRVVEPKRA 78

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

 Score = 55.5 bits (133), Expect = 3e-10
 Identities = 28/81 (34%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           KK+FVGGI     E   +D+F ++G +   +I+ D  + + RGFGF+TFD    VD ++ 
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 117 KGNKLELAGAQVEVKKAEPKK 137
           +     + G   EV+KA  ++
Sbjct: 61  QKYH-TINGHNAEVRKALSRQ 80

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

 Score = 57.0 bits (137), Expect = 4e-10
 Identities = 44/128 (34%), Positives = 67/128 (52%), Gaps = 10/128 (7%)

Query: 49  VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
           +GS    + K+F+GG+    ++   +D F  FGDV + +++ D  T RSRGFGF+ F+ E
Sbjct: 27  LGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDE 86

Query: 109 QAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGG 168
            A    +++ +  EL G  + V  A   +P+ P+             G G+    GGYGG
Sbjct: 87  GAATAAISEMDGKELNGRHIRVNPAN-DRPSAPRAYGG---------GGGYSGGGGGYGG 136

Query: 169 GGFAGGGF 176
           GG  GGGF
Sbjct: 137 GGDGGGGF 144

Length = 144

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

 Score = 54.7 bits (131), Expect = 5e-10
 Identities = 28/78 (35%), Positives = 50/78 (64%), Gaps = 3/78 (3%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 115
           +K+F+GG+     ++  +  F Q+G + +  +MRD +T RSRGFGF+T+ + + VD  + 
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 116 AKGNKLELAGAQVEVKKA 133
           A+ +K++  G  VE K+A
Sbjct: 63  ARPHKVD--GRVVEPKRA 78

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

 Score = 54.2 bits (131), Expect = 8e-10
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +  S  +D+ ++FF + G+V + +I +D    RS+GFG + F TE+     L K 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60

Query: 119 NKLELAGAQVEVKKAEPK 136
            + EL G ++ V  A  +
Sbjct: 61  GE-ELLGREIRVDLATER 77

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

 Score = 53.9 bits (130), Expect = 9e-10
 Identities = 20/46 (43%), Positives = 28/46 (60%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 46
           KD KTGQ +GFGFV +AD     KV+   H+I+G+  ++K    K
Sbjct: 32 KKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMIDGRWCDVKIPNSK 77

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|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 = 54.0 bits (130), Expect = 1e-09
 Identities = 22/55 (40%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST--SRSRGFGFITFDTEQA 110
           K+FVG IP S +E + ++ F Q+G V +  ++RD S    +S+G  F+TF T +A
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57

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

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD-------TEQAV 111
           I++G +P    E E K +F QFG V+  ++ R   T  S+ +GFI F          +++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 112 DDLLAKGNKLE 122
           ++ L  G  L+
Sbjct: 62  NNYLLMGKVLQ 72

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|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 = 53.1 bits (128), Expect = 2e-09
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAV 111
           ++FV  +P +  E+E ++ F  FG++ E  +  D  T RS+GF F++F   E AV
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV 55

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

 Score = 52.7 bits (126), Expect = 3e-09
 Identities = 23/60 (38%), Positives = 39/60 (65%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+     E++ +++F  FG+V+  ++  D+ T++ RGF FITF  E+ V  ++ K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

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

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 21/82 (25%), Positives = 49/82 (59%), Gaps = 9/82 (10%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDL 114
           ++V  +   +++++ K+ F ++G +   ++M+D    +S+GFGF+ F+     ++AV++L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEEL 62

Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
               N  E+ G ++ V +A+ K
Sbjct: 63  ----NGKEVNGKKLYVGRAQKK 80

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

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +I V  +P  V ED  ++ F   G+V + ++MR     +SR FGF+ F +E+     +  
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 118 GNK 120
            NK
Sbjct: 61  FNK 63

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

 Score = 52.2 bits (126), Expect = 4e-09
 Identities = 22/76 (28%), Positives = 45/76 (59%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIF+GG+P+ ++ED+ K+    FG ++   +++D +T  S+G+ F  +      D  +A 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 118 GNKLELAGAQVEVKKA 133
            N ++L   ++ V++A
Sbjct: 62  LNGMQLGDKKLTVQRA 77

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

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

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 22/47 (46%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPK 46
          MKD  T + RGFGFVT+A  S VD  +    H ++G++VE KR +P+
Sbjct: 32 MKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGREVEPKRAVPR 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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 56.4 bits (136), Expect = 6e-09
 Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 8/102 (7%)

Query: 45  PKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
              +    D K  +I++G +P  + ED+ K+    FGD++   +++D +T  S+G+ F  
Sbjct: 285 LVNSTTVLDSK-DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCE 343

Query: 105 F----DTEQAVDDLLAK---GNKLELAGAQVEVKKAEPKKPN 139
           +     T+ A+  L  K    NKL +  A V   +A     N
Sbjct: 344 YKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSN 385

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

>gnl|CDD|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 = 51.1 bits (123), Expect = 9e-09
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
           +FVG IP    E++  + F + G V   +++ D  T + +G+GF  F+       A+ +L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

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

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 18/52 (34%), Positives = 30/52 (57%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           +FVGG+  SV E + ++ F +FG V + +I++       RGF +I   T +A
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA 53

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

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 18/48 (37%), Positives = 33/48 (68%), Gaps = 1/48 (2%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           ++FV  IP S  E++ ++ F +FGD++   I++D +T  S+GFG++ F
Sbjct: 3   RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKR 42
          M+D  TG+ RGFGFVT+   S V++V       + GKQVE+KR
Sbjct: 32 MQDHDTGRSRGFGFVTFDSESAVERVFSAGMLELGGKQVEVKR 74

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

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 22/47 (46%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDK-VIEDTHIINGKQVEIKRTIPK 46
          M+DR++G+ RGF FVT+ D   VDK V++  H ING   E+K+ + K
Sbjct: 33 MEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSK 79

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 21/42 (50%), Positives = 30/42 (71%), Gaps = 1/42 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDK-VIEDTHIINGKQVEIK 41
          + D++TG+ RGF FVT+ D   VDK V++  H ING +VE+K
Sbjct: 32 VTDKETGKKRGFAFVTFDDYDPVDKIVLQKYHTINGHRVEVK 73

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +P  + E+E +  F   GDV+  +I+RD  T   +GFG++ F T+ +V   L   
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL- 60

Query: 119 NKLELAGAQVEVK 131
           N ++L G ++ VK
Sbjct: 61  NGIKLKGRKIRVK 73

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 18/74 (24%), Positives = 41/74 (55%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
             +FVG +     E+  ++ F ++GD++  +++RD  T  S+G+ F+ ++ E+       
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 117 KGNKLELAGAQVEV 130
             +KL + G+++ V
Sbjct: 64  DAHKLVIDGSEIFV 77

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

 Score = 50.1 bits (119), Expect = 2e-08
 Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
           D KT  I V  +P ++ ++EFK  F   G+++  +++RD  T +S G+GF+ +      D
Sbjct: 1   DSKTNLI-VNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDAD 59

Query: 113 DLLAKGNKLELAGAQVEVKKAEP 135
             +   N L+L    ++V  A P
Sbjct: 60  KAINTLNGLKLQTKTIKVSYARP 82

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

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

 Score = 53.8 bits (128), Expect = 3e-08
 Identities = 30/142 (21%), Positives = 58/142 (40%), Gaps = 22/142 (15%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP------------- 45
           ++DR+TG+ RGF FV +      +K IE  +   + G+ + +++  P             
Sbjct: 148 VRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLD 207

Query: 46  -----KGAVG--SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSR 98
                K + G      K+  ++VG +P    E+E  D F   GD+    +         +
Sbjct: 208 ASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPK 267

Query: 99  GFGFITFDTEQAVDDLLAKGNK 120
              F+  +  +   +  ++GNK
Sbjct: 268 SRSFVGNEASKDALESNSRGNK 289

Length = 306

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

 Score = 54.4 bits (131), Expect = 3e-08
 Identities = 42/191 (21%), Positives = 80/191 (41%), Gaps = 32/191 (16%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVG---SKD---- 53
           MKD  +G+ RGF FV +       K +E+   +NGK++ + +   K  VG    +     
Sbjct: 211 MKD-GSGRSRGFAFVNFEKHEDAAKAVEE---MNGKKIGLAKEGKKLYVGRAQKRAEREA 266

Query: 54  -----FKTKK-----------IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRS 97
                F+  +           ++V  +  +V +++ ++ F + G++   ++M D     S
Sbjct: 267 ELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVS 325

Query: 98  RGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLP----QPSYRRYNNPKP 153
           RGFGF+ F   +  +  + + +   L G  + V  A+ K+        Q    +    + 
Sbjct: 326 RGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQL 385

Query: 154 AYGSGFGDAYG 164
             GS  G A G
Sbjct: 386 PMGSPMGGAMG 396

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

 Score = 49.6 bits (118), Expect = 3e-08
 Identities = 25/75 (33%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+GG+     + + KD+F +FG+V +  +  D  T RSRGFGF+ F   ++VD ++ + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 59

Query: 119 NKLELAGAQVEVKKA 133
            + +L G  ++ K+A
Sbjct: 60  KEHKLNGKVIDPKRA 74

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|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 = 49.5 bits (119), Expect = 3e-08
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 6/70 (8%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++VG +P  + E+E +  F  FG ++E ++ +D      +G+ F+ FDT +A    +   
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 119 NKLELAGAQV 128
           N   + G  V
Sbjct: 57  NGTSINGQTV 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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 49.8 bits (119), Expect = 4e-08
 Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGA 48
          MKD+ T + RGFGFV + DP+ V  V+    H ++G+ ++ K   P+G 
Sbjct: 32 MKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGRTIDPKPCTPRGM 80

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

 Score = 49.6 bits (118), Expect = 4e-08
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+    ++ +  ++  +FG+V +  I  D  T RSRGFGF+ F    +VD +   
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKV--- 57

Query: 118 GNKLELAGAQVEVKKAEPKK 137
              LEL   +++ K  +PK+
Sbjct: 58  ---LELKEHKLDGKLIDPKR 74

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +F+G +   V+E    D F  FG  +Q  +IMRD  T  S+GF FI++D+ +A D  +  
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 118 GNKLELAGAQVEVKKA 133
            N   L    + V  A
Sbjct: 64  MNGQYLCNRPITVSYA 79

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

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

 Score = 49.1 bits (117), Expect = 5e-08
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVGG+     + + K++F +FG+V +  I  D  T RSRGFGF+ F    +V+ +L + 
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQ- 59

Query: 119 NKLELAGAQVEVKKA 133
            + +L G  ++ K+A
Sbjct: 60  KEHKLDGRVIDPKRA 74

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

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 23/43 (53%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
          M D++T + RGFGFVT+    VVDKV E   H IN K VE K+
Sbjct: 32 MFDKQTNRHRGFGFVTFESEDVVDKVCEIHFHEINNKMVECKK 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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 48.9 bits (116), Expect = 7e-08
 Identities = 21/58 (36%), Positives = 36/58 (62%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           K+FVGG+     E++ K++F  FG+++  ++  D  T+  RGF F+T+  E+ V  LL
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL 58

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|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 48.8 bits (116), Expect = 7e-08
 Identities = 22/60 (36%), Positives = 35/60 (58%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           + ++FVG +P  ++E E K+FFM FG+V E +I       +   FGF+ FD  + V  +L
Sbjct: 5   SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRIL 64

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSR---GFGFITFDTEQAVDDL 114
           +I+V  +   ++ED+ +  F +FG+V+  +I +     + R   GF F+TF    + ++ 
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 115 LAKGNKLELAGAQVEV 130
           L      EL G ++ V
Sbjct: 62  LQLNGT-ELGGRKISV 76

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

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

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            +FVG +  SV+++  K  F +FG V   +++ D  T RSRGFG++ F++ +     +  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 118 GNKLELAGAQVEVKKA 133
            +  EL G  + V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

 Score = 48.7 bits (117), Expect = 8e-08
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQI--MRDHSTSRSRGFGFITFDTEQ---A 110
           T  + + G+     E++          V    +  +RD  T  SRGF F+ F + +    
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 111 VDDLLAKGNKLELAGAQVEVKKA 133
             D L   +   + G  V V  A
Sbjct: 62  WMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 52.9 bits (127), Expect = 9e-08
 Identities = 34/143 (23%), Positives = 67/143 (46%), Gaps = 15/143 (10%)

Query: 2   KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKK- 58
           +D  T +  G+G+V + +P+  ++ +E  +   + GK + I           +D   ++ 
Sbjct: 34  RDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRI-------MWSQRDPSLRRS 86

Query: 59  ----IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
               IFV  +  SV+     D F +FG++   ++  D    +SRG+GF+ F+ E++    
Sbjct: 87  GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAA 145

Query: 115 LAKGNKLELAGAQVEVKKAEPKK 137
           + K N + L   +V V +   K 
Sbjct: 146 IQKVNGMLLNDKEVYVGRFIKKH 168

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

 Score = 48.4 bits (115), Expect = 9e-08
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 11/68 (16%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++FVG +P+ + E++FK  F ++G+  E  I RD      RGFGFI  ++       LA+
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRT-----LAE 51

Query: 118 GNKLELAG 125
             K EL G
Sbjct: 52  IAKAELDG 59

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|214636 smart00360, RRM, RNA recognition motif

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 10/42 (23%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEI 40
          ++D++TG+ +GF FV +      +K +E  +   ++G+ +++
Sbjct: 32 VRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 3/87 (3%)

Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQA 110
           KD    K+FVG IP ++ E + +  F QFG + E  +++D  T   +G  F+T+   E A
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 111 VDDLLAKGNKLELAGAQ--VEVKKAEP 135
           +    A   +  L G    ++VK A+ 
Sbjct: 61  LKAQSALHEQKTLPGMNRPIQVKPADS 87

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 47.5 bits (114), Expect = 1e-07
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 73  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 132
               F  FG+V++ ++++        GF F+ F TE+A +  +   N +   G  + V  
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 133 A 133
           +
Sbjct: 56  S 56

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 18/41 (43%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 3  DRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKR 42
          D+KT + RGF F+T+     V K++E   H+I GK+VE+K+
Sbjct: 34 DKKTNKRRGFCFITFDSEEPVKKILETQFHVIGGKKVEVKK 74

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 20/42 (47%), Positives = 31/42 (73%), Gaps = 1/42 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIK 41
          M+D  T + RGFGFVT++DP+ VDKV+    H ++GK+++ K
Sbjct: 31 MRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKIDPK 72

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

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 9  PRGFGFVTYADPSVVDKVIEDTHIINGKQVEI 40
           R F FVT+ADP V   +  + HII G  V +
Sbjct: 36 FRAFAFVTFADPEVAQSLCGEDHIIKGVSVHV 67

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 23/52 (44%), Positives = 32/52 (61%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           ++VGGIP    EDE + +F   G+++E  +M    T R RG  FITF TE+A
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEA 52

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

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 5/81 (6%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           + ++FVG +P  V++ E K+FF Q+G+V E   +R +S  +   FGF+ FD  + V  +L
Sbjct: 3   SHQLFVGNLPHDVDKSELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEPVQKIL 59

Query: 116 AKGNKLELAGAQVEVKKAEPK 136
              N+  +    V +   E K
Sbjct: 60  --SNRPIMFRGDVRLNVEEKK 78

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAK 117
           ++V G+P ++ + E +  F Q+G +   +I+RD  T  SRG GFI FD   +A + +   
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 118 GNKLELAGAQ 127
             +     ++
Sbjct: 63  NGQKPEGASE 72

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 17/53 (32%), Positives = 33/53 (62%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           +FV  +   V E +  +FF + G V++ +I+RD ++ RS+G  ++ F  E++V
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54

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

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 17/70 (24%), Positives = 35/70 (50%)

Query: 64  IPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL 123
           +P  + ++E +  F   G ++  +I+RD  T +S G+GF+ +  E      +   N  E+
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 124 AGAQVEVKKA 133
              +++V  A
Sbjct: 68  RNKRLKVSYA 77

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 15/48 (31%), Positives = 31/48 (64%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           +IFVG + + V ++     F ++   Q+ +++RD  T +S+G+GF++F
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSF 55

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

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           IFVG +   V +      F  F    + ++M D  + RSRG+GF++F    D E A++++
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 115 LAK 117
             K
Sbjct: 62  NGK 64

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|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 = 47.2 bits (113), Expect = 2e-07
 Identities = 13/52 (25%), Positives = 30/52 (57%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           +F+  +P+   + +    F  FG+V   ++  D +T +S+ FGF+++D  ++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPES 52

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFVG +   V ++E  + F + G + E  ++     + +  F FI F+ EQA    +   
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 119 NKLELAGAQVEVKKAE 134
           N   L    + V+  E
Sbjct: 64  NHSMLKNKTMHVQYKE 79

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAV 111
           T ++FV  +P S  ED+ +  F +FG++ E  +  D  + +S+GF ++ F D E AV
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAV 58

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 15/59 (25%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +FV  +  SV EDE +  F + G++ + ++++++   +S+G+ ++ F+ E++V + L  
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKL 59

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

 Score = 47.1 bits (113), Expect = 3e-07
 Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 4/55 (7%)

Query: 64  IPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           +    +ED+ ++ F  FG +    + +D  T +SRGF F+TF    D E+A++ L
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKL 61

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G +++ Q++ D  T RSRGFGF+ F++   V+D  AK  K
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VED--AKEAK 58

Query: 121 LELAGAQV 128
             L G ++
Sbjct: 59  ERLNGMEI 66

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

 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVG +P +   +E +  F ++G V E  ++++        +GF+  + E+  +D +  
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA 52

Query: 118 GNKLELAGAQVEVK 131
            N  E  G ++ V+
Sbjct: 53  LNGYEFMGKRINVE 66

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

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

 Score = 50.8 bits (121), Expect = 4e-07
 Identities = 46/188 (24%), Positives = 78/188 (41%), Gaps = 21/188 (11%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR-TIPKGAVGSKDFKTKKI 59
           M+D KTG   G+ FV +   +   + I+    +NG  V  KR  +     G +  K   +
Sbjct: 140 MRDYKTGYSFGYAFVDFGSEADSQRAIK---NLNGITVRNKRLKVSYARPGGESIKDTNL 196

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKG 118
           +V  +P ++ +D+    F ++G + +  I+RD  T   RG  F+ F+  E+A + + A  
Sbjct: 197 YVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256

Query: 119 NKLELAGAQ-VEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFG 177
           N +   G+Q + V+ AE                   A    +    G    G    G  G
Sbjct: 257 NVIPEGGSQPLTVRLAEEH---------------GKAKAHHYMSQMGHGNMGNMGHGNMG 301

Query: 178 GSGGGGGG 185
            +GG G  
Sbjct: 302 MAGGSGMN 309

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

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

 Score = 46.4 bits (110), Expect = 4e-07
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVG +P    E E +  F Q+G V E  I+++        +GF+  D + A D+ +  
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53

Query: 118 GNKLELAGAQVEVK 131
            +  +L G  + V+
Sbjct: 54  LHHYKLHGVAINVE 67

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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 46.6 bits (110), Expect = 4e-07
 Identities = 27/88 (30%), Positives = 48/88 (54%), Gaps = 9/88 (10%)

Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DT 107
           +D KT  I V  +P ++ ++E K  F   G+++  +++RD  T +S G+GF+ +    D 
Sbjct: 1   EDSKTNLI-VNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 59

Query: 108 EQAVDDLLAKGNKLELAGAQVEVKKAEP 135
           E+A++ L    N L L    ++V  A P
Sbjct: 60  EKAINTL----NGLRLQTKTIKVSYARP 83

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 9/83 (10%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQA 110
           KT  I V  +P ++ +DE +  F   G+++  +++RD  T +S G+GF+ +    D E+A
Sbjct: 1   KTNLI-VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59

Query: 111 VDDLLAKGNKLELAGAQVEVKKA 133
           ++ L    N L L    ++V  A
Sbjct: 60  INTL----NGLRLQNKTIKVSYA 78

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

 Score = 46.0 bits (109), Expect = 7e-07
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           +K+FVG +    NE++ +  F  FG ++E  ++RD +  +SRG  F+TF + Q 
Sbjct: 2   RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQC 54

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

 Score = 45.7 bits (108), Expect = 9e-07
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-A 116
           K+FVG +P ++ E E +  F + G+V E  I++D  T   +G  F+ + T    D  + A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 117 KGNKLELAG--AQVEVKKAE 134
             N+  L G  + V+V+ A+
Sbjct: 61  LHNQRTLPGGASPVQVRYAD 80

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

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 17/58 (29%), Positives = 35/58 (60%), Gaps = 4/58 (6%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 112
           IFVG +   ++ +  +  F  FG++ + ++++D  T +S+G+GF++F    D E A+ 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ 59

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

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           + V  +P ++ +DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 115 LAKGNKLELAGAQVEVKKAEP 135
               N L L    ++V  A P
Sbjct: 64  ----NGLRLQSKTIKVSYARP 80

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 8/81 (9%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           + V  +P ++ ++EF+  F   G+++  +++RD  T +S G+GF+ +    D E+A++ L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 115 LAKGNKLELAGAQVEVKKAEP 135
               N L L    ++V  A P
Sbjct: 65  ----NGLRLQTKTIKVSYARP 81

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDL 114
           ++V G+P ++ + E +  F  +G +   +I+ D+ T  SRG GFI FD     E+A+  L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 115 LAKGNKLELAGAQVEVKKA 133
              G     A   + VK A
Sbjct: 63  --NGTIPPGATEPITVKFA 79

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 11/71 (15%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++FVG +P+ + E+EFK+ F ++G+V E  +      ++ +GFGFI  DT        A+
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRT-----NAE 51

Query: 118 GNKLELAGAQV 128
             K EL G   
Sbjct: 52  KAKAELDGIMR 62

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

 Score = 48.4 bits (115), Expect = 2e-06
 Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 9/87 (10%)

Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTE 108
           + KT  I V  +P ++ ++E +  F   G+++  +++RD  T +S G+GF+ +    D E
Sbjct: 1   ESKTNLI-VNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAE 59

Query: 109 QAVDDLLAKGNKLELAGAQVEVKKAEP 135
           +AV+ L    N L L    ++V  A P
Sbjct: 60  KAVNSL----NGLRLQNKTIKVSYARP 82

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 15/50 (30%), Positives = 29/50 (58%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
           +++G +P    E E + +F QFG V   ++ R   T +S+G+ F+ F++ 
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 10/80 (12%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVDDLL 115
           K ++V  +P S  E++ ++ F ++G+V+  + ++D        + F+ F + + AV   +
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAV-KAM 52

Query: 116 AKGNKLELAGAQVEVKKAEP 135
            + N  EL G+ +EV  A+P
Sbjct: 53  EEMNGKELEGSPIEVSLAKP 72

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

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

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +IFVG IP  + EDE    F + G + + ++M D  T  +RG+ F+TF T++A  + +  
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 118 GNKLEL 123
            N  E+
Sbjct: 63  YNNHEI 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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++FVG +P+ + EDEFK  F ++G+  E  I      ++ +GFGFI  ++    +   A+
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56

Query: 118 GNKLELAGAQVEVK 131
            +   + G Q+ V+
Sbjct: 57  LDDTPMRGRQLRVR 70

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 22/74 (29%), Positives = 38/74 (51%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++VG +   V E+   + F+Q G V    I +D  T   +G+GF+ F +E+  D  +   
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 119 NKLELAGAQVEVKK 132
           N ++L G  + V K
Sbjct: 61  NMIKLYGKPIRVNK 74

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFV  +P SV   + KD F + G+V    +  D+   RS+GFG + F++ +     +   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 119 NKLELAGAQVEVK 131
           N  +L G ++EV+
Sbjct: 60  NGYDLEGRELEVR 72

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

>gnl|CDD|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 = 2e-06
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++FVG +P  + E+E +  F ++G   E  I +D      +GFGFI  +T    +   A+
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 118 GNKLELAGAQVEVK 131
            + + L G Q+ V+
Sbjct: 57  LDNMPLRGKQLRVR 70

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

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 15/48 (31%), Positives = 28/48 (58%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 106
           ++V  +P  + EDE +  F  +G++ +  ++RD ST   RG  F+ +D
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYD 50

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

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG IP  + EDE    F + G + E ++M D S   +RG+ F+T+  ++A    + + 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVKQL 62

Query: 119 NKLELAGAQ 127
           +  E+   +
Sbjct: 63  HNYEIRPGK 71

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

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

 Score = 43.8 bits (103), Expect = 4e-06
 Identities = 20/45 (44%), Positives = 29/45 (64%), Gaps = 1/45 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDK-VIEDTHIINGKQVEIKRTI 44
          M DR +G+ RGF FVT+ D   VDK VI+  H +NG   E+++ +
Sbjct: 33 MTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL 77

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 42
          ++DR TGQ  G+GFV Y D +   K I     +NG ++  KR
Sbjct: 33 VRDRITGQSLGYGFVDYVDENDAQKAIN---TLNGFEIRNKR 71

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           +FVGGI   ++E E + FF ++G V+E +I+ D  T  S+G+GF++F    D ++ V+  
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 115 LA-KGNKLELAGA 126
           +   G KL+L  A
Sbjct: 67  INFHGKKLKLGPA 79

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 67  SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD-TEQA 110
           SV ED+ ++ F  FG++Q+  +++D  T  S+G  ++ F     A
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSA 57

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

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 21/72 (29%), Positives = 40/72 (55%)

Query: 64  IPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL 123
           +P ++ ++EF+  F+  G V+  +I+RD  T  S GFGF+ + + +     +   N L+L
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 124 AGAQVEVKKAEP 135
              +++V  A P
Sbjct: 68  QNKRIKVAYARP 79

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

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

 Score = 47.0 bits (112), Expect = 5e-06
 Identities = 29/55 (52%), Positives = 29/55 (52%)

Query: 171 FAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRG 225
             GGGFGG  GGG GGG       G RGGG GG    G  GG GG GGG G   G
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

>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 = 43.2 bits (102), Expect = 6e-06
 Identities = 23/75 (30%), Positives = 38/75 (50%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG IP    E++ KD F + G V   +++ D  T + +G+GF  +  ++     +   
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 119 NKLELAGAQVEVKKA 133
           N  EL G Q+ V  A
Sbjct: 61  NGYELNGRQLRVDNA 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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 7/51 (13%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFG----DVQEHQIMRDHSTSRSRGFGFITF 105
           I + G+P SV E++ ++  +  G    DV+   +MR  +T  SRGF F+ F
Sbjct: 5   IMLRGLPLSVTEEDIRNALVSHGVEPKDVR---LMRRKTTGASRGFAFVEF 52

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

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

 Score = 43.1 bits (102), Expect = 6e-06
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG + + V E+   + F+Q G ++  +I +D +  + + F F+TF  E +V   +   
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQLL 62

Query: 119 NKLELAGAQVEVK 131
           N + L G ++ +K
Sbjct: 63  NGIRLFGRELRIK 75

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

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

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 17/58 (29%), Positives = 28/58 (48%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           +FV  +P    E+     F +FG V+    + D ST R++G GF+ F  +   +  L 
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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

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

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           V  +      D+ +  F ++G+V +  I RD  T  SRGF F+ F    D E A+D +
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

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

 Score = 43.1 bits (101), Expect = 8e-06
 Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 107
           +K+F+G +    NE++ +  F  FG ++E +I+R      SRG  F+TF T
Sbjct: 2   RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRG-PDGLSRGCAFVTFTT 51

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQA 110
            ++V  +  S++++  ++ F  FG +   ++M D    RS+GFGF+ F + E+A
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEA 55

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

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

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           +VG +   V E    + F   G V   ++ RD  T RS G+ ++ F    D E+A+D L
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

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

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

 Score = 43.1 bits (101), Expect = 8e-06
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA-- 116
           +++ G+P ++ + + +D F +FG +   +++ D +T  SRG  FI FD     ++ +   
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 117 KGNKLELAGAQVEVKKA 133
            G+K   +   + VK A
Sbjct: 63  NGHKPPGSSEPITVKFA 79

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|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 14/95 (14%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF-------- 102
           SKD     ++ G +P  V +++ ++FF  +   QE  I R    S+              
Sbjct: 1   SKD----TVYCGKLPKKVTDEDLREFFKDYNP-QEIWIFR-TRKSKRNPLQLHRHFTAAL 54

Query: 103 ITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 137
           +T DTE+ +D+++      +L G ++ +K A   K
Sbjct: 55  VTLDTEETLDEIIESLKSKKLNGKKISLKPAYLSK 89

This subfamily corresponds to the RRM2 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 93

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

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
          M D+ T + RGFGFVT+    +V+KV E   H IN K VE K+
Sbjct: 32 MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK 74

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

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 20/45 (44%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 3  DRKTGQPRGFGFVTYADPSVVDK-VIEDTHIINGKQVEIKRTIPK 46
          D++TG+ RGFGFV + +    DK  +   H ING +VE+K+ +PK
Sbjct: 34 DKQTGKKRGFGFVYFQNHDSADKAAVVKFHPINGHRVEVKKAVPK 78

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 8/76 (10%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
           I++GG+P  + E +    F Q+G++ +  ++RD  T +S+GF F+ ++    T  AVD+L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 115 LAKGNKLELAGAQVEV 130
               N ++L G  + V
Sbjct: 72  ----NGIKLLGRTIRV 83

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++ V  +P  + ED+ +  F  FG + + Q+       + R FGF+ + TE+     L  
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60

Query: 118 GNK 120
            N 
Sbjct: 61  FNN 63

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

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           +   ++V G+P ++ + E +  F Q+G +   +I+ D  T  SRG GFI FD     ++ 
Sbjct: 1   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

Query: 115 LAKGNKLELAGA 126
           +   N  + +GA
Sbjct: 61  IKGLNGQKPSGA 72

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 11/42 (26%), Positives = 25/42 (59%)

Query: 69  NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
            +++ +  F +FG ++  +++RD  T  S  + FI F+T++ 
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED 57

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAK 117
           + VG +P    +++F++    FG V+   ++   ST  S+G+GF+ + +   A   L A 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASA---LKA- 57

Query: 118 GNKLELAGAQVEVKKA 133
             K +L G Q+  +K 
Sbjct: 58  --KNQLDGKQIGGRKL 71

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           K++ V  IP    + + +  F QFG + + +I+ +   S+  GFGF+TF          A
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSK--GFGFVTFANSAD-----A 53

Query: 117 KGNKLELAGAQVEVKKAE 134
              + +L G  VE +K E
Sbjct: 54  DRAREKLHGTVVEGRKIE 71

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

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 66  SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG 125
           S   E++  ++F QFG V + +I       + R FGF+TF+  + V  +L+KGN   + G
Sbjct: 9   SRFTEEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTFENAETVKRILSKGNPHFICG 64

Query: 126 AQVEVK 131
           ++V VK
Sbjct: 65  SRVRVK 70

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|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 = 41.8 bits (99), Expect = 2e-05
 Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 3/42 (7%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 42
          MKD +TG+ RGFGFVT+      D  I D   +NGK++E + 
Sbjct: 34 MKDPETGESRGFGFVTFESVEDADAAIRD---LNGKELEGRV 72

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 20/47 (42%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDK-VIEDTHIINGKQVEIKRTIPK 46
          + DR++G+ RGFGFVT+ D   VDK V++  H ING   E+++ + +
Sbjct: 33 ITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSR 79

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
           ++V G+P ++++ E +  F Q+G +   +I+ D  T  SRG GFI FD     E+A+  L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 42.5 bits (99), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           +   ++V G+P ++ + E +  F Q+G +   +I+ D  T  SRG GFI FD     ++ 
Sbjct: 4   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

Query: 115 LAKGNKLELAGA 126
           +   N  +  GA
Sbjct: 64  IKGLNGQKPPGA 75

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 9/77 (11%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDD 113
           ++ V  +P    E + K  F  FG V E  I R     + +GF F+ F    D E+A+  
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 114 LLAKGNKLELAGAQVEV 130
           +    N  ++ G  V V
Sbjct: 60  V----NGKKIKGRPVAV 72

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 16/46 (34%), Positives = 27/46 (58%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
           IFV  +P   +E      F  FG V   +++RD +T++ +G+GF+T
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVT 49

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|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +IF+G +P  + EDE      + G + E ++M D +   +RG+ F+TF  +Q   + + +
Sbjct: 3   EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQ 61

Query: 118 GNKLEL 123
            N  E+
Sbjct: 62  LNNYEI 67

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 13/27 (48%), Positives = 18/27 (66%)

Query: 2  KDRKTGQPRGFGFVTYADPSVVDKVIE 28
          KD++TGQ RGF FVT+      ++ IE
Sbjct: 33 KDKETGQSRGFAFVTFHTREDAERAIE 59

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.3 bits (105), Expect = 3e-05
 Identities = 28/55 (50%), Positives = 28/55 (50%)

Query: 168 GGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGA 222
           G G   GG  G G GGGGGG R  G  G   GG  G G GG  GG GG GGG   
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 13/82 (15%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           +FV  I S+V ++E +  F QFGD++       ++  + RGF  +++       +A   L
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTL-----YTACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
                  EL G ++++  + PK
Sbjct: 59  ----QGTELGGRKLDIHFSIPK 76

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

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

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 19/73 (26%), Positives = 37/73 (50%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +++VG I   + ED  +  F  FG ++   +  D  T + +GF F+ ++  +A    L +
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 118 GNKLELAGAQVEV 130
            N + L G  ++V
Sbjct: 62  MNGVMLGGRNIKV 74

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 13/77 (16%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDL 114
           ++VGG+   V E + +D F QFG++      R  +    +   F+TF T    E+A + L
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEI------RSITVVPRQQCAFVTFTTREAAEKAAERL 57

Query: 115 LAKGNKLELAGAQVEVK 131
               NKL + G ++++K
Sbjct: 58  F---NKLIINGRRLKLK 71

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

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 22/43 (51%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
          M D+ T + RGFGFVT+ +  VV+KV E   H IN K VE K+
Sbjct: 36 MFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKK 78

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

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 18/31 (58%), Positives = 23/31 (74%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH 31
          M+D  T + RGFGFVT+ADP+ VDKV+   H
Sbjct: 32 MRDPTTKRSRGFGFVTFADPASVDKVLAQPH 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFVG +      +E ++ F   G +    I+ D  T + +GF +I F  + +V++ L   
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLL- 60

Query: 119 NKLELAGAQVEV 130
           N+ E  G Q++V
Sbjct: 61  NESEFRGRQIKV 72

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

>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR--SRGFGFITFDTEQAVDDL 114
           +K+FVGG+P  ++EDE    F +FG +      +  S S    +G+ F+ F  E +V  L
Sbjct: 1   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 60

Query: 115 L 115
           +
Sbjct: 61  I 61

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

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

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 54  FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
           FKT  +FV  +     E + +  F ++G ++  +++RD  T + RG+ FI F+ E+
Sbjct: 1   FKT--LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 54

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

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 17/78 (21%), Positives = 39/78 (50%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
             ++V  +  +   D+ +  F ++G + +  I  D  T R RGF ++ F+  +  +D L 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 117 KGNKLELAGAQVEVKKAE 134
             ++    G ++E++ A+
Sbjct: 61  YLDRTRFLGREIEIQFAQ 78

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM--RDHST-SRSRGFGFITF----DTE 108
           T  ++VG +   V E+     F +FG +   +IM  R      R+R  GF+ F    D E
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 109 QAVDDL 114
           +A+D+L
Sbjct: 61  RALDEL 66

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 18/83 (21%), Positives = 40/83 (48%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+  +P    + +    FM FG+V   ++  D  T+ S+ FGF+++D   +    +   
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 119 NKLELAGAQVEVKKAEPKKPNLP 141
           N  ++   +++V+    K  + P
Sbjct: 70  NGFQIGMKRLKVQLKRSKNDSKP 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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
           ++FVG IP  + EDE    F + G + + ++M D  + ++RG+ FITF  ++A  +
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQE 58

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R 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; it binds RNA through its RRM domains. . Length = 79

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

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKR 42
          M D  T + RGFGF+T++     D+ +E   H I+G Q+E+KR
Sbjct: 35 MVDPNTKRSRGFGFITFSSADEADEAMEAQPHSIDGNQIELKR 77

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

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 19/72 (26%), Positives = 35/72 (48%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFV G+     E++  D F +FG+++   +  D  T   +G+  I ++T++     +   
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 119 NKLELAGAQVEV 130
           N  EL G  + V
Sbjct: 69  NGKELLGQTISV 80

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

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 15/58 (25%)

Query: 64  IPSSVNEDEFKDFFMQFGD---------VQEHQIMRD------HSTSRSRGFGFITFD 106
           +P SV+E + K+ F++            +++ +IMRD      +   +S+G+GF+ F 
Sbjct: 8   LPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFT 65

This subfamily corresponds to the RRM4 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 = 98

>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 = 40.5 bits (95), Expect = 6e-05
 Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
            K+FV G+P SV ++E +  F + G V+  +++ + S  + +G  ++ ++ E +    + 
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVL 61

Query: 117 KGNKLELAGAQVEVKKAEP 135
           K +  E+    + V  + P
Sbjct: 62  KMDGTEIKEKTISVAISNP 80

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS----RSRGFGFITFDTEQAVDD 113
           ++++G + S + E      F ++G +++      H +     + RG+ F+TF+T++  + 
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFD-FLFHKSGPLKGQPRGYCFVTFETKEEAEK 59

Query: 114 LLAKGNKLELAGAQVEVKKA 133
            L   N     G ++ V+ A
Sbjct: 60  ALKSLNGKTALGKKLVVRWA 79

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

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

 Score = 43.6 bits (103), Expect = 9e-05
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           ++VG +   V E +  D F  FG V   ++ RD  T RS G+G++ F    D E+A++ +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

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

 Score = 40.4 bits (94), Expect = 9e-05
 Identities = 19/70 (27%), Positives = 36/70 (51%)

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N 
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 121 LELAGAQVEV 130
           +EL G ++ V
Sbjct: 74  MELDGRRIRV 83

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

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

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 18/70 (25%), Positives = 36/70 (51%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +    +ED   + F ++G++   ++  D  + R +GFG++ F +++A    L   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 119 NKLELAGAQV 128
              +L G  V
Sbjct: 61  GGTDLLGRPV 70

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 14/57 (24%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD-TEQAV 111
           + ++F+  +  +  E++ +  F ++G + E  +  D  T + +GF F+T+   E AV
Sbjct: 2   SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAV 58

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           + +FVG +   V E+   + F+Q G + +  I +D    + + FGF+ F   ++V   +A
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA 60

Query: 117 KGNKLELAGAQVEVK 131
             N + L G  ++V 
Sbjct: 61  LLNGIRLYGRPIKVH 75

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

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 17/72 (23%), Positives = 36/72 (50%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++V G+ S+    + K  F ++G V   +I+ +  +  +R FGF+T  + +     +   
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 119 NKLELAGAQVEV 130
           ++ EL G  + V
Sbjct: 62  HRTELHGRVISV 73

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF---DTEQAVDDL 114
           K+FVG +     E E ++ F  +G V++  +MRD    +SRG  F+ +   +  QA    
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 115 L 115
           L
Sbjct: 60  L 60

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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRD--HSTSRSRGFGFITFDTEQA 110
           I VGGI  S++ED+ K+FF   G+V   ++  D  HS      F F+ F   ++
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR----FAFVEFADAES 52

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 19/75 (25%), Positives = 41/75 (54%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +   +  D+ K  F  FG + + ++++D +T +S+G+GF++F  +   ++ + + 
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 119 NKLELAGAQVEVKKA 133
               L G Q+    A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           +FVG +P     ++    F   G     +++ D  T +S+G  F+ FDT +A+   L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL 59

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

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FV  +     E +  +FF + G V++ Q ++D ++ RS+G  ++ F   ++V   LA  
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT 151

Query: 119 NKLELAGAQVEVKKAEPKK 137
            ++ L G  + V+ ++ +K
Sbjct: 152 GQM-LLGRPIIVQSSQAEK 169

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 15/37 (40%), Positives = 26/37 (70%), Gaps = 1/37 (2%)

Query: 2  KDRKTGQPRGFGFVTYADPSVVDKVIEDTH-IINGKQ 37
           DR+TG+ RG+GFVT+ D    ++  +D + II+G++
Sbjct: 34 TDRQTGKSRGYGFVTFKDKESAERACKDPNPIIDGRK 70

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 20/41 (48%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 3  DRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKR 42
          D  TG+ RGFGFV + D + VDKV+E   H ++GK ++ KR
Sbjct: 34 DPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKR 74

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 18/75 (24%), Positives = 40/75 (53%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +   +  ++ K  F  FG + + ++++D +T +S+G+GF++F  +   ++ +   
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 119 NKLELAGAQVEVKKA 133
               L G Q+    A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 22/81 (27%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQ--------EHQIMRDHSTSRS----------- 97
           +K+FVGG+P  + E +  + F +FG +Q        E +   D S               
Sbjct: 1   RKVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60

Query: 98  ---RGFGFITFDTEQAVDDLL 115
              +G+ F+ F+ E++V  LL
Sbjct: 61  QHPKGYVFLLFEKERSVRSLL 81

This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 112

>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 14/81 (17%)

Query: 64  IPSSVNEDEFKDFFMQFGDVQEH-------QIMRDHSTSRSRGFGFITFDTEQ-AVDDLL 115
           +P +  E + +      G +QEH       ++MR+ S+ +SRGF F+ F+  Q A   + 
Sbjct: 10  LPQNATETDIR------GQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWME 63

Query: 116 AKGNKLELAGAQVEVKKAEPK 136
           A  + L + G +V +  ++PK
Sbjct: 64  ANQHSLMILGQKVSMHYSDPK 84

This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 85

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 58  KIFVGGIPSSVNEDEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           ++F+  IP  +   + KD F  + G+V   ++ +D    +SRG G + F  +++V   L 
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKALE 59

Query: 117 KGNKLELAGAQVEVKK 132
             N+ EL G ++ VK+
Sbjct: 60  TMNRYELKGRKLVVKE 75

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

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 12/52 (23%), Positives = 31/52 (59%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           +++ G+P +  +++ +     FG +   + + D  T++ +G+GF+ FD+ +A
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.0 bits (90), Expect = 2e-04
 Identities = 17/89 (19%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 50  GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
           G        +++ G+P +  + +       +G +   + + D +T++ +G+GF+ FD+  
Sbjct: 1   GWDQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPA 60

Query: 110 AVDDLLAKGNKLELAGAQVEVKKAEPKKP 138
           A    ++    L+ +G Q ++ K + + P
Sbjct: 61  AAQKAVS---ALKASGVQAQMAKQQEQDP 86

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQV 38
          + DR+TG+ RGFGFV        +  IE    +NG   
Sbjct: 32 ITDRETGRSRGFGFVEMETAEEANAAIEK---LNGTDF 66

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK 46
          M+D  T + RGFGFVTY+    VD  +    H ++G+ VE KR + +
Sbjct: 35 MRDPNTKRSRGFGFVTYSSVEEVDAAMNARPHKVDGRVVEPKRAVSR 81

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

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 3  DRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
          D  TG+ RGFGFV + D + V+KV++   H ++G+ ++ KR
Sbjct: 33 DPVTGRSRGFGFVLFKDAASVEKVLDQKEHKLDGRVIDPKR 73

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 27/48 (56%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 156 GSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGG 203
           G G G   GG GGGG  GGG GG  GGG G G    G  G RGGG GG
Sbjct: 7   GGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRG--RGGGGGGRGGGGGG 52

Length = 293

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
            K+ V  +P    + E ++ F  FG V+  ++ +       RGF F+ F T+Q  
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEA 54

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|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 27/59 (45%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 162 AYGGYGGGGFA-GGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGG 219
           A GG+GG  F  GGGFGG G GG G  +  +  +    G  GG G+G  FGG    GGG
Sbjct: 79  AGGGFGGRRFDGGGGFGGFGTGGDGAEFNLNDLFD-AAGRGGGGGIGDLFGGLFNRGGG 136

Length = 392

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 2/43 (4%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIK 41
          +   K G+ +GF FV +  P   +K +E  +   ++G+++++ 
Sbjct: 30 IVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72

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

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 3  DRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKR 42
          D  TG+ RGFGF+ + D S V+KV+E   H ++G+ ++ K+
Sbjct: 34 DPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDGRLIDPKK 74

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 15/52 (28%), Positives = 30/52 (57%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           +++G +   ++E      F + G+V   +I+R+  T +S G+GF+ F T +A
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEA 53

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 18/79 (22%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           K +FV  + ++V E+  +  F +FG ++  + ++D        + F+ F+   A    + 
Sbjct: 2   KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMD 53

Query: 117 KGNKLELAGAQVEVKKAEP 135
           + N  E+ G ++E+  A+P
Sbjct: 54  EMNGKEIEGEEIEIVLAKP 72

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R 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 R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|221115 pfam11456, DUF3019, Protein of unknown function (DUF3019)

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 8/50 (16%)

Query: 103 ITFDTEQAVD-DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNP 151
           + FD+++ +   L+   +   LA A+V+V    PKK        RR  NP
Sbjct: 57  LEFDSDKDIQFVLIDSDSNQPLASAKVKVTWVSPKKR-------RRRRNP 99

This is a bacterial family of uncharacterized proteins. Length = 102

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRG-FGFITFDTEQAVDDLLAK 117
           +FV G     +E++  D+F  FG V    + +D      +G +  + FD+++ VD +L++
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKVLSE 58

Query: 118 GNKLELAGAQVEVKKAE 134
                L G ++ V+  E
Sbjct: 59  PQHT-LNGHRLRVRPRE 74

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

>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 = 38.0 bits (89), Expect = 4e-04
 Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQF-GDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVD 112
           ++ V  +P+S+ E E K+ F +  G++ + +++R     +SR   FI +   E+A  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG-KSRRIAFIGYKTEEEAQK 57

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|236092 PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional

 Score = 40.4 bits (95), Expect = 4e-04
 Identities = 26/57 (45%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 167 GGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVG----GEFGGYGGYGGG 219
           GGGG  GGGFGG GGG GGGG    G     GGG                 GG+GGG
Sbjct: 124 GGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGG 180

Length = 186

>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 = 38.1 bits (89), Expect = 4e-04
 Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
            +  +++G +   V E++ K+ F ++G++Q   ++        RG  ++  +T Q     
Sbjct: 1   CSTTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRA 54

Query: 115 LAKGNKLELAGAQVEV 130
           L K   ++LAG +++V
Sbjct: 55  LQKLRNVKLAGKKIKV 70

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

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K++VG +     + E +D F ++G ++   + R        GF F+ F+  +  +D +  
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 118 GNKLELAGAQVEVKKA 133
            +   + G +V V+ +
Sbjct: 56  LDGRRICGNRVRVELS 71

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

 Score = 37.8 bits (87), Expect = 5e-04
 Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKRTIPK 46
          M+D +T + RGFGFVTY+    VD  +    H ++G+ VE KR + +
Sbjct: 35 MRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDGRVVEPKRAVSR 81

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

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

Query: 1  MKDRKTGQPRGFGFVTYADP----SVVDKVIEDTHI-INGKQVEI 40
          ++D+ TG  RGF FV +         +D +       I+G+ V +
Sbjct: 37 IRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRV 81

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

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

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++ G  P+S    + K  F   G V++  ++    +   +   FITF+  +A    +   
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57

Query: 119 NKLELAGAQVEVKK 132
           N   + G  ++V++
Sbjct: 58  NGASVDGNCIKVQR 71

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|215598 PLN03138, PLN03138, Protein TOC75; Provisional

 Score = 41.4 bits (97), Expect = 5e-04
 Identities = 22/57 (38%), Positives = 25/57 (43%)

Query: 133 AEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYR 189
           A          +    N       +      GG GGGGF G G GG GGGGGGGG+R
Sbjct: 49  ASASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWR 105

Length = 796

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++++G +P    E + + FF  +G ++E         +   GFGF+ F+  +  DD + +
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIRE--------INLKNGFGFVEFEDPRDADDAVYE 52

Query: 118 GNKLELAGAQVEVKKAEP 135
            N  EL G +V V+ A  
Sbjct: 53  LNGKELCGERVIVEHARG 70

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQA 110
           ++V  +P +   +  K  F ++G V    + R   T   +GF FI F+T E+A
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEA 54

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 107
           IFV  +   V   + K+ F   G V    I  D    +SRG G + F+ 
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEH 48

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

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +++  +P  ++E + +     +G V   +I+RD S  +SRG GF   ++ +  +D+++K 
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKF 61

Query: 119 NKLELAGA 126
           N   L G 
Sbjct: 62  NGKYLKGE 69

This subfamily corresponds to the RRM2 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, they 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 = 79

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           ++V  +P S+  ++    F ++G V +  I++D  T +S+G  FI F    D  + V  L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 115 LAKGNKLELAGAQVEVKKA 133
               N  EL G  ++   A
Sbjct: 64  ----NNKELFGRTLKCSIA 78

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

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 65  PSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 124
           P  ++ED+ +D    FG     ++M      ++    F TFD EQA    L++ ++L++ 
Sbjct: 8   PPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNT--AFATFDNEQAASQALSRLHQLKIL 64

Query: 125 GA--QVE 129
           G    VE
Sbjct: 65  GKRLVVE 71

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

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 19/76 (25%), Positives = 40/76 (52%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FV  +  +   ++ +  F ++G + +  +  D  T R RGF +I F+  +  +D L   
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 119 NKLELAGAQVEVKKAE 134
           N+  + G Q+E++ A+
Sbjct: 63  NRKWVCGRQIEIQFAQ 78

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 2  KDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQ 37
          KD  TG  +G+ F  Y DPSV D+ I     +NG Q
Sbjct: 34 KDSATGLSKGYAFCEYLDPSVTDQAIAG---LNGMQ 66

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

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 15/78 (19%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFG-FITF----DTEQAVDD 113
           + V  + S +++ E +  F QFG+V      +D   +  R    F+ F      E A+D 
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEV------KDIRETPLRPSQKFVEFYDIRAAEAALDA 57

Query: 114 LLAKGNKLELAGAQVEVK 131
           L    N     G +++VK
Sbjct: 58  L----NGRPFLGGRLKVK 71

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

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

 Score = 37.1 bits (87), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IF+  +  S++     D F  FG++   ++  D +   S+G+GF+ F+TE+A    + K 
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENG-GSKGYGFVHFETEEAAVRAIEKV 63

Query: 119 NKLELAGAQVEV 130
           N + L   +V V
Sbjct: 64  NGMLLNDKKVFV 75

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

>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +++G IPS +   E KD F  FG+++E  I   H  S    +GF+T+   +     +  G
Sbjct: 5   VYIGKIPSRMTRSELKDRFSVFGEIEECTI---HFRSEGDNYGFVTYRYTEEAFAAIENG 61

Query: 119 NKLELAGAQ 127
           +KL      
Sbjct: 62  HKLRRPDEL 70

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

 Score = 37.1 bits (87), Expect = 8e-04
 Identities = 16/73 (21%), Positives = 39/73 (53%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           + VG +  +VN+D  K+ F  +G V++  +  D   +  RG+ ++ F++ +  +  +   
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 119 NKLELAGAQVEVK 131
           +  ++ G +V V+
Sbjct: 61  DGGQIDGQEVTVE 73

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.9 bits (85), Expect = 9e-04
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           K +FV  + ++V E+  +  F QFG ++  + ++D        + FI FD        + 
Sbjct: 2   KVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 53

Query: 117 KGNKLELAGAQVEVKKAEP 135
           + N  EL G  +E+  A+P
Sbjct: 54  EMNGKELEGENIEIVFAKP 72

This subgroup corresponds to the RRM3 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 that is 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 = 72

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 6  TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVE 39
          TG+ +GF FV + D    +K +E  +   + G+++ 
Sbjct: 35 TGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70

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

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 19/41 (46%), Positives = 27/41 (65%), Gaps = 1/41 (2%)

Query: 3  DRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKR 42
          D  TG+ RGFGFV + +   VDKV++   H +NGK ++ KR
Sbjct: 33 DPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKR 73

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 13/28 (46%), Positives = 18/28 (64%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE 28
          + DR+TG+ RGFG+V +  P    K IE
Sbjct: 32 ITDRETGRSRGFGYVDFESPEDAKKAIE 59

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 5/61 (8%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDD 113
           ++FVG IP  V EDE    F   G + E ++M D    ++RG+ F+ +    + ++AV +
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVRE 61

Query: 114 L 114
           L
Sbjct: 62  L 62

This subgroup corresponds to the RRM1 of RBM47, 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, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517)

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 16/52 (30%), Positives = 18/52 (34%)

Query: 168 GGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGG 219
           GG   GG F             S G  G  G   GG+G       +G  GGG
Sbjct: 5   GGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGG 56

This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown. Length = 280

>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           K++ +  IP  V++   +D   +FG+   +    DH  SR+  F F   +    ++ ++ 
Sbjct: 1   KRLRITNIPLDVSDYTIEDLIKEFGEP-VYSKFYDHKDSRTAVFEF---EDPSILEKVVE 56

Query: 117 KGNKLELAGAQVEV 130
           K N  EL GA++EV
Sbjct: 57  KYNGKELNGAKIEV 70

This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 15/48 (31%), Positives = 29/48 (60%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 106
           +F+  +P    + E    F+ FG+V   ++  D +T++S+ FGF++FD
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFD 54

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 59  IFVGGIPSSVNE-DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
           IFVG +   VNE D    F  +F   +  +IM D  T  SRG+GF+ F  E
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDE 54

This subgroup corresponds to the RRM2 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 = 80

>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown]

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 22/58 (37%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 168 GGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEF--GGYGGYGGGMGAY 223
           GG   GG F    G   G         G  GGGY G G G  F   G GG GG  G +
Sbjct: 50  GGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGIF 107

Length = 334

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
           ++FVG IP  + EDE    F + G + E ++M + S   +RG+ F+ + T++
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFS-GENRGYAFVMYTTKE 53

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), 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 = 78

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 18/76 (23%), Positives = 39/76 (51%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FV  I      ++ +  F ++G + +  +  D  T R RGF ++ F+  +  +D L   
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 119 NKLELAGAQVEVKKAE 134
           ++  + G Q+E++ A+
Sbjct: 63  DRKWICGRQIEIQFAQ 78

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +++  +P S++E E ++    FG V   +I+RD S+  SRG GF   ++ +  + +++  
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 119 N 119
           N
Sbjct: 62  N 62

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQ-FGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
           IFVG +   V +   ++ F   +  V+  +++ D  T RS+G+GF+ F  E
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDE 54

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 50/146 (34%), Positives = 57/146 (39%), Gaps = 16/146 (10%)

Query: 152 KPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYG--------VRGGGYGG 203
           K    S      GGY GGG  G     + G G GGG                V GGG G 
Sbjct: 58  KGEDNSSNNMVKGGYNGGGDGGNDNSSNDGSGSGGGATDIRLNENSLKSRIIVAGGGGGS 117

Query: 204 YGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSG 263
              G   GG GG+GGG+    G   +   +   GG           GG      G  G+G
Sbjct: 118 ---GNYNGGSGGFGGGLVGGGG---TSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNG 171

Query: 264 VGGGGGYGGGPSGYDIGLGSSYGGSS 289
            GGGGGY GG  G+  G G   GGSS
Sbjct: 172 GGGGGGYFGGGGGHYAGGGG--GGSS 195

This family of proteins is greatly expanded in Trichomonas vaginalis. The proteins are composed of several glycine rich motifs interspersed through the sequence. Although many proteins have been annotated by similarity in the family these annotations given the biased composition of the sequences these are unlikely to be functionally relevant. Length = 248

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 18/42 (42%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 41
          M+D  T + RGFGFVT+ D + VDKV+  + H ++ K ++ K
Sbjct: 33 MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 17/41 (41%), Positives = 27/41 (65%), Gaps = 3/41 (7%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 41
          ++D+ TGQ  G+GFV Y DP+  DK I   + +NG +++ K
Sbjct: 36 VRDKITGQSLGYGFVNYVDPNDADKAI---NTLNGLKLQTK 73

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

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 31/63 (49%), Positives = 31/63 (49%), Gaps = 9/63 (14%)

Query: 156 GSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGG 215
           G GFG   GG  GGG  GG  GG  GGG GGG         RG G GG G G   GG GG
Sbjct: 3   GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGG---------RGRGRGGGGGGRGGGGGGG 53

Query: 216 YGG 218
            G 
Sbjct: 54  PGK 56

Length = 293

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRS-RGFGFITFDTEQ 109
           KI V  IP      E ++ F  FG+++  ++ +  + + S RGFGF+ F T+Q
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQ 54

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|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 28/51 (54%), Positives = 29/51 (56%)

Query: 158 GFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGG 208
           G G + GG GGG   G G GG GGGGG GG   SG  G R  G GG G GG
Sbjct: 110 GRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGG 160

Length = 182

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 19/70 (27%), Positives = 35/70 (50%)

Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G +    ++ D  T RSRGF F+ F+      + +   N 
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 121 LELAGAQVEV 130
           +EL G ++ V
Sbjct: 64  MELDGRRIRV 73

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 36.3 bits (83), Expect = 0.002
 Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDL 114
           +++ G+P    + +       +G +   + + D +T++ +G+GF+ FD+    ++AV  L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 115 LAKGNKLELAGAQ 127
            A G + ++A  Q
Sbjct: 67  KANGVQAQMAKQQ 79

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal Mei2-like proteins

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 10/29 (34%), Positives = 17/29 (58%)

Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQ 84
          T+ + V G+P  V+    K+ F + GDV+
Sbjct: 1  TRYLKVTGVPKDVSTSNLKEIFEKMGDVK 29

This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 72

>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 22/58 (37%), Positives = 26/58 (44%)

Query: 250 GGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSS 307
           GG     GG+GG G G GGG GGG  G   G G +   +     + S    GG GG  
Sbjct: 124 GGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGD 181

Length = 186

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +++G + S VNE + +  F      +EH+I       +  G+ F+    +   D  + K 
Sbjct: 1   LYIGNLSSDVNESDLRQLF------EEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKL 54

Query: 119 NKLELAGAQVEVKKAEPKK 137
           N   L G  +EV+ + PKK
Sbjct: 55  NGKILQGKVIEVEHSVPKK 73

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 15/73 (20%), Positives = 37/73 (50%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+  +P    + +    F+ FG+V   ++  D  T+ S+ FGF+++D   +    +   
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 119 NKLELAGAQVEVK 131
           N  ++   +++V+
Sbjct: 67  NGFQIGTKRLKVQ 79

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

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 12/61 (19%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDD 113
           +++V   P   +E   ++ F  +G V+E +++          F F+ F       +A D 
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 114 L 114
           +
Sbjct: 53  V 53

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

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 3/82 (3%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           + +F   + + +   + +DFF   G V++ +I+ D ++ RS+G  ++ F   Q+V   LA
Sbjct: 2   RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP--LA 59

Query: 117 KG-NKLELAGAQVEVKKAEPKK 137
            G     L G  + V+ ++ +K
Sbjct: 60  IGLTGQRLLGVPIIVQASQAEK 81

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

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

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 10/50 (20%), Positives = 29/50 (58%), Gaps = 6/50 (12%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           ++ +++G +P S +E+E ++   +FG + + +I+++      +   F+ F
Sbjct: 3   SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHF 46

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

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 1  MKDRKTGQPRGFGFVTYADP 20
          + D +TG+ RG+GFVT+A  
Sbjct: 32 VTDPETGESRGYGFVTFAML 51

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

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPK 46
          M+D  + + RGFGFVT++  + VD  +    H I+G+ VE KR + +
Sbjct: 35 MRDPASKRSRGFGFVTFSCMNEVDAAMAARPHTIDGRVVEPKRAVAR 81

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|236092 PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 24/61 (39%), Positives = 29/61 (47%)

Query: 152 KPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFG 211
           + + G G G   GG+GGGG   GG GG GGGGG  G   + A       +      G FG
Sbjct: 119 RASRGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFG 178

Query: 212 G 212
           G
Sbjct: 179 G 179

Length = 186

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 13/78 (16%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDD 113
           ++ V G+P   +  + KDF  Q GDV    + RD       G G + F    D E+A+  
Sbjct: 2   RVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRD-----QEGEGVVEFTSQEDMERALRK 56

Query: 114 LLAKGNKLELAGAQVEVK 131
           L    +  E  G +V V+
Sbjct: 57  L----DGTEFRGRRVRVE 70

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           +FVG +     EDE +  F + G ++  ++M    + + +GF F+ F+  +   + L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           FVG +P +  + +    F     V+  +++RD  T + +GF ++ F+    V+ L     
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFED---VESLK---E 57

Query: 120 KLELAGAQVEVKK 132
            LE  GA  + + 
Sbjct: 58  ALEYDGALFDDRS 70

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 10/55 (18%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFK 55
          ++++ TG P G+ FV +AD +  ++ +   H +NGK       IP G+   K FK
Sbjct: 33 IRNKLTGGPAGYCFVEFADEATAERCL---HKLNGK------PIP-GSNPPKRFK 77

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	314
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.91
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.89
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.89
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.87
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.87
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.86
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.86
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.85
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.85
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.82
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.82
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.81
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.81
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.8
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.79
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.78
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.78
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.77
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.74
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.73
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.73
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.69
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.69
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.68
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.68
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.67
KOG0122	270	consensus Translation initiation factor 3, subunit	99.67
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.66
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.66
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.64
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.63
PLN03120	260	nucleic acid binding protein; Provisional	99.63
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.62
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.59
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.59
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.59
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.58
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.56
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.55
PLN03213	759	repressor of silencing 3; Provisional	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.54
smart00362	72	RRM_2 RNA recognition motif.	99.54
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.54
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.53
smart00360	71	RRM RNA recognition motif.	99.52
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.51
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.5
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.5
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.49
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.49
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.48
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.47
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.43
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.39
smart00361	70	RRM_1 RNA recognition motif.	99.37
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.36
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.31
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.31
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.29
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.29
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.25
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.24
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.21
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.19
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.19
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.18
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.18
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.16
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.15
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.14
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.11
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.09
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.09
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.05
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.05
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.04
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.03
KOG0226	290	consensus RNA-binding proteins [General function p	99.03
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	99.01
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.96
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.96
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.88
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.87
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.87
KOG4210	285	consensus Nuclear localization sequence binding pr	98.85
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.83
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.77
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.73
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.71
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.68
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.68
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.68
KOG1855	484	consensus Predicted RNA-binding protein [General f	98.67
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.64
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.57
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.57
KOG0151	877	consensus Predicted splicing regulator, contains R	98.49
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.47
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.47
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.47
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.39
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.34
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.33
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.18
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.09
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.99
smart00361	70	RRM_1 RNA recognition motif.	97.99
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.92
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.88
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.86
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.86
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	97.85
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.81
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.81
KOG4207	256	consensus Predicted splicing factor, SR protein su	97.76
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	97.75
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.72
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	97.68
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	97.66
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.64
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.59
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	97.57
KOG2314	698	consensus Translation initiation factor 3, subunit	97.57
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.52
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.52
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	97.43
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	97.4
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.37
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.37
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	97.37
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	97.37
smart00360	71	RRM RNA recognition motif.	97.37
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	97.32
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	97.3
KOG3152	278	consensus TBP-binding protein, activator of basal	97.27
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.23
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.21
KOG2591	684	consensus c-Mpl binding protein, contains La domai	97.14
PLN03213	759	repressor of silencing 3; Provisional	97.12
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	97.08
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	97.0
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.0
PLN03120	260	nucleic acid binding protein; Provisional	96.88
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.85
smart00362	72	RRM_2 RNA recognition motif.	96.77
KOG0226	290	consensus RNA-binding proteins [General function p	96.72
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	96.54
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.42
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	96.37
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.37
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.31
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.17
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.16
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.93
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.89
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	95.55
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.45
KOG2135	526	consensus Proteins containing the RNA recognition	95.37
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.34
PLN03121	243	nucleic acid binding protein; Provisional	95.3
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.2
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.09
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	95.03
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.73
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	94.44
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	94.41
KOG4210	285	consensus Nuclear localization sequence binding pr	94.35
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.2
KOG4660	549	consensus Protein Mei2, essential for commitment t	93.82
KOG4483	528	consensus Uncharacterized conserved protein [Funct	93.74
KOG1995	351	consensus Conserved Zn-finger protein [General fun	93.61
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	93.56
KOG2318	650	consensus Uncharacterized conserved protein [Funct	93.4
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	93.13
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.54
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	92.52
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	92.24
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	91.56
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	91.24
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	89.98
KOG2891	445	consensus Surface glycoprotein [General function p	89.32
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	88.67
smart00596	69	PRE_C2HC PRE_C2HC domain.	88.24
KOG4213	205	consensus RNA-binding protein La [RNA processing a	87.33
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	86.81
KOG2314	698	consensus Translation initiation factor 3, subunit	86.22
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	85.1
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	83.82
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	83.09
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	82.35
KOG0533	243	consensus RRM motif-containing protein [RNA proces	82.27
PF02714	325	DUF221: Domain of unknown function DUF221; InterPr	80.93

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=7.6e-28  Score=222.26  Aligned_cols=135  Identities=23%  Similarity=0.524  Sum_probs=120.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+|+.|+++||||||+|+++++|++||+  +..+|.+++|+|.++.+..    +....++|||.|||++++|++|+++|+
T Consensus       140 ~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~----~~~~~~~lfV~nLp~~vtee~L~~~F~  215 (346)
T TIGR01659       140 MRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGG----ESIKDTNLYVTNLPRTITDDQLDTIFG  215 (346)
T ss_pred             EecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccccc----cccccceeEEeCCCCcccHHHHHHHHH
Confidence            4788999999999999999999999998  4458889999998876542    233467899999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeecCCCCCC
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKAEPKKPN  139 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a~~~~~~  139 (314)
                      +|++|++|+|++|+.++++|+||||+|+++++|++||++||+++|.+  ++|+|++|+.....
T Consensus       216 ~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       216 KYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             hcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            99999999999999999999999999999999999999999998876  78999998876443

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).

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

Probab=99.92  E-value=3.7e-24  Score=208.04  Aligned_cols=139  Identities=24%  Similarity=0.482  Sum_probs=121.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC-------CCCCCCcceEEEcCCCCCCCHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV-------GSKDFKTKKIFVGGIPSSVNED   71 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~-------~~~~~~~~~l~V~nLp~~~~e~   71 (314)
                      |+|+.|+++||||||+|+++++|++||+  +...|.++.|+|.+.......       .......++|||+|||++++++
T Consensus       140 ~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vtee  219 (612)
T TIGR01645       140 SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSET  219 (612)
T ss_pred             eecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHH
Confidence            5788999999999999999999999998  455889999999865433211       1122345799999999999999


Q ss_pred             HHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295           72 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        72 ~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      +|+++|++||+|++|+|++|+.++++||||||+|++.++|++||+.||.++|.++.|+|.++......
T Consensus       220 dLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       220 DIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             HHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999998865443

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.91  E-value=5.3e-24  Score=182.33  Aligned_cols=133  Identities=23%  Similarity=0.503  Sum_probs=119.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCCC------------CCCCCcceEEEcCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAVG------------SKDFKTKKIFVGGIPS   66 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~~------------~~~~~~~~l~V~nLp~   66 (314)
                      |||.+|.+||||+||.|.+.++|+.||..+  .-|..|.|+..|++.|....            ....+.++|||+||+.
T Consensus        95 irD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~  174 (321)
T KOG0148|consen   95 IRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIAS  174 (321)
T ss_pred             eecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCc
Confidence            789999999999999999999999999954  47889999999988775322            1456788999999999


Q ss_pred             CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295           67 SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        67 ~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      .++|++|+++|+.||+|.+|+|.++      ++||||.|++.|+|.+||..+|+.+|.++.|++.|-+.....
T Consensus       175 ~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  175 GLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             cccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            9999999999999999999999987      689999999999999999999999999999999998876543

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

Probab=99.90  E-value=7.9e-23  Score=197.43  Aligned_cols=137  Identities=28%  Similarity=0.523  Sum_probs=120.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC--------CCCCCcceEEEcCCCCCCCHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG--------SKDFKTKKIFVGGIPSSVNED   71 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~--------~~~~~~~~l~V~nLp~~~~e~   71 (314)
                      |+|+.|+++||||||+|.+.++|++||+ +...+.++.|.|+.+.......        ......++|||.|||.+++|+
T Consensus       122 ~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~  201 (457)
T TIGR01622       122 IKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQ  201 (457)
T ss_pred             eecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHH
Confidence            5788999999999999999999999998 5568889999988754332111        112336899999999999999


Q ss_pred             HHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           72 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        72 ~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      +|+++|++||+|+.|.|+.+..++++++||||+|.++++|++||+.||++.|.+++|+|.++....
T Consensus       202 ~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~  267 (457)
T TIGR01622       202 ELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDST  267 (457)
T ss_pred             HHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCC
Confidence            999999999999999999999999999999999999999999999999999999999999988543

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=99.90  E-value=8.9e-23  Score=190.54  Aligned_cols=80  Identities=25%  Similarity=0.407  Sum_probs=77.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      +|||.|||++++|++|+++|++||.|++|+|++|+.|+++||||||+|++.++|.+||+.||+..|.+++|+|.++..+.
T Consensus       271 ~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       271 CIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999998775

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

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

Probab=99.89  E-value=1.2e-21  Score=190.19  Aligned_cols=126  Identities=23%  Similarity=0.416  Sum_probs=110.2

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCCCC-CCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAVGS-KDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~~~-~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      .+.++++||||+|++.++|++|++++    ..++++.|.|+++.++....+ ...+.++|||+|||++++|++|+++|++
T Consensus       177 ~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~  256 (578)
T TIGR01648       177 DKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSE  256 (578)
T ss_pred             ccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHh
Confidence            45689999999999999999999743    257899999999887755443 2345689999999999999999999999


Q ss_pred             c--CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           80 F--GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        80 ~--G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      |  |+|++|+++++        ||||+|+++++|++||+.||+.+|++++|+|++|++...
T Consensus       257 f~~G~I~rV~~~rg--------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       257 FKPGKVERVKKIRD--------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             cCCCceEEEEeecC--------eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            9  99999988744        999999999999999999999999999999999987644

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.89  E-value=4e-22  Score=186.16  Aligned_cols=133  Identities=28%  Similarity=0.569  Sum_probs=118.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+|+.|+++||||||+|.++++|++||+  +...|.++.|.|+++.++..    .....+|||.|||.+++|++|+++|+
T Consensus        36 ~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~----~~~~~~l~v~~l~~~~~~~~l~~~f~  111 (352)
T TIGR01661        36 VRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD----SIKGANLYVSGLPKTMTQHELESIFS  111 (352)
T ss_pred             EEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc----ccccceEEECCccccCCHHHHHHHHh
Confidence            5788999999999999999999999998  44588999999998866432    33567899999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeecCCCC
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKAEPKK  137 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a~~~~  137 (314)
                      +||+|+.+.|+.+..++.+++||||+|++.++|++||+.||+..+.+  ++|.|+++....
T Consensus       112 ~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       112 PFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             ccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            99999999999998888999999999999999999999999998876  678888886554

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=7.9e-23  Score=185.02  Aligned_cols=137  Identities=27%  Similarity=0.475  Sum_probs=114.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc---cCccCCcE--EEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED---THIINGKQ--VEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKD   75 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~---~~~i~g~~--i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~   75 (314)
                      ||||.|+.+||||||+|.+.++|.+|+..   ..++.+..  |.|+.+....   +....+++|||+-|+..++|+||++
T Consensus        67 ~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~---er~~~e~KLFvg~lsK~~te~evr~  143 (510)
T KOG0144|consen   67 IKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGER---ERIVEERKLFVGMLSKQCTENEVRE  143 (510)
T ss_pred             ecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhh---hccccchhhhhhhccccccHHHHHH
Confidence            79999999999999999999999988874   34555544  4444443221   2225678999999999999999999


Q ss_pred             HHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee-e--CCeEEEEeecCCCCCCCC
Q 021295           76 FFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE-L--AGAQVEVKKAEPKKPNLP  141 (314)
Q Consensus        76 ~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~-~--~gr~l~V~~a~~~~~~~~  141 (314)
                      +|++||.|++|.|++| ..+.+||||||+|++.|.|..||+.||... +  +..+|.|++|.+++++..
T Consensus       144 iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  144 IFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            9999999999999999 578899999999999999999999998754 4  458899999999887543

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

Probab=99.87  E-value=1.2e-21  Score=191.55  Aligned_cols=134  Identities=19%  Similarity=0.365  Sum_probs=113.5

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC-------------------------CCCCCCcc
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV-------------------------GSKDFKTK   57 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~-------------------------~~~~~~~~   57 (314)
                      ..+.++++||||+|.+.++|++||+ +...|.++.|.|.+.......                         .......+
T Consensus       217 ~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (509)
T TIGR01642       217 VNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKD  296 (509)
T ss_pred             EEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCC
Confidence            3456789999999999999999997 555788888888653321100                         00123457


Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      +|||+|||+.+++++|+++|++||.|+.|.|+++..+++++|||||+|+++++|++||+.||++.|.+++|.|++|....
T Consensus       297 ~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~  376 (509)
T TIGR01642       297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGA  376 (509)
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999986543

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

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.87  E-value=6.6e-22  Score=179.84  Aligned_cols=127  Identities=24%  Similarity=0.410  Sum_probs=114.2

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHccC----ccCCcEEEEeecCCCCCCCC-CCCCcceEEEcCCCCCCCHHHHHHHHhcc
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIEDTH----IINGKQVEIKRTIPKGAVGS-KDFKTKKIFVGGIPSSVNEDEFKDFFMQF   80 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~~~----~i~g~~i~v~~~~~~~~~~~-~~~~~~~l~V~nLp~~~~e~~l~~~F~~~   80 (314)
                      +.++||||||+|.+..+|..|.+++.    .+++..+.|+|+.+...... ...+.+.|||.||+.++|||.|+++|++|
T Consensus       204 k~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~  283 (506)
T KOG0117|consen  204 KTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEF  283 (506)
T ss_pred             cccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhc
Confidence            67999999999999999888877442    78899999999998866544 45678999999999999999999999999


Q ss_pred             CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCC
Q 021295           81 GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  140 (314)
Q Consensus        81 G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~  140 (314)
                      |+|++|+.++|        ||||.|.+.++|.+|++.+|..+|++..|+|.+|++.....
T Consensus       284 G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  284 GKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             cceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            99999999977        99999999999999999999999999999999999876543

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

Probab=99.86  E-value=5e-21  Score=189.44  Aligned_cols=133  Identities=25%  Similarity=0.487  Sum_probs=115.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      ++|+.|++++|||||+|.+.++|++|++  +...|.++.|+|.|+.....  .......+|||.|||.++++++|+++|+
T Consensus        33 ~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~--~~~~~~~~vfV~nLp~~~~~~~L~~~F~  110 (562)
T TIGR01628        33 CRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPS--LRRSGVGNIFVKNLDKSVDNKALFDTFS  110 (562)
T ss_pred             EecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccccc--ccccCCCceEEcCCCccCCHHHHHHHHH
Confidence            4788899999999999999999999998  44568999999988754322  2223456899999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      +||+|+.|+|+.+ .++++++||||+|+++++|++||++||+..+.++.|.|.....+
T Consensus       111 ~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628       111 KFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             hcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            9999999999988 47789999999999999999999999999999999998765443

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

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=6.7e-21  Score=173.30  Aligned_cols=129  Identities=24%  Similarity=0.462  Sum_probs=110.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--Ccc-CCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HII-NGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFF   77 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i-~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F   77 (314)
                      |+|+-++.+||||||+|++.++|++|++.+  ++| .+|.|.|..++          ..++|||+|||.+.+++||++.|
T Consensus       116 MmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv----------an~RLFiG~IPK~k~keeIlee~  185 (506)
T KOG0117|consen  116 MMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV----------ANCRLFIGNIPKTKKKEEILEEM  185 (506)
T ss_pred             eecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee----------ecceeEeccCCccccHHHHHHHH
Confidence            789999999999999999999999999943  444 68888888765          35899999999999999999999


Q ss_pred             hccCC-eEEEEEeecC-CCCCcceEEEEEeCChHHHHHHHHhc--CCeeeCCeEEEEeecCCCCCC
Q 021295           78 MQFGD-VQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        78 ~~~G~-v~~v~i~~~~-~~g~~rG~afV~F~~~~~a~~a~~~l--~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      ++.++ |++|.|..+. ++.++||||||+|+++.+|..|..+|  ..+.++++.|.|+||.++...
T Consensus       186 ~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~  251 (506)
T KOG0117|consen  186 KKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEP  251 (506)
T ss_pred             HhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCC
Confidence            99976 6677666553 35678999999999999999999876  557799999999999998653

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

Probab=99.85  E-value=2.5e-20  Score=151.81  Aligned_cols=85  Identities=32%  Similarity=0.661  Sum_probs=80.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ...+++|||.|||++++|++|+++|++||+|++|+|+.|+.|+++++||||+|+++++|++||+.||+++|++++|+|++
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            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 021295          133 AEPKK  137 (314)
Q Consensus       133 a~~~~  137 (314)
                      +.++.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            88654

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

Probab=99.85  E-value=7e-21  Score=188.40  Aligned_cols=133  Identities=23%  Similarity=0.477  Sum_probs=115.8

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccC----CcEEEEeecCCCCCCC--------------CCCCCcceEEEcCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIIN----GKQVEIKRTIPKGAVG--------------SKDFKTKKIFVGGI   64 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~----g~~i~v~~~~~~~~~~--------------~~~~~~~~l~V~nL   64 (314)
                      .++++||||||+|++.++|++|++  +...|.    ++.+.|.++..+....              .......+|||.||
T Consensus       214 ~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl  293 (562)
T TIGR01628       214 GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNL  293 (562)
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCC
Confidence            578999999999999999999998  444666    7888887765543221              12345678999999


Q ss_pred             CCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           65 PSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        65 p~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      ++++++++|+++|++||+|++|+|+.| .++++++||||+|+++++|++||+.||+..|.+++|.|.+|..+..
T Consensus       294 ~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~  366 (562)
T TIGR01628       294 DDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ  366 (562)
T ss_pred             CCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHH
Confidence            999999999999999999999999999 6899999999999999999999999999999999999999988754

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

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.85  E-value=1.5e-21  Score=175.80  Aligned_cols=142  Identities=46%  Similarity=0.823  Sum_probs=131.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCC--CCCCcceEEEcCCCCCCCHHHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGS--KDFKTKKIFVGGIPSSVNEDEFKDFF   77 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~--~~~~~~~l~V~nLp~~~~e~~l~~~F   77 (314)
                      |+|+.|+++|+|.||+|++++.+.++|. ..|+|+++.|+++.+++++....  ....+++|||+.||.+++|++|++.|
T Consensus        39 m~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yf  118 (311)
T KOG4205|consen   39 MRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYF  118 (311)
T ss_pred             eccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhh
Confidence            7899999999999999999999999998 67889999999999999987665  34468999999999999999999999


Q ss_pred             hccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCCCCC
Q 021295           78 MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQP  143 (314)
Q Consensus        78 ~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~~~~  143 (314)
                      ++|+.|.++.|+.|..+.++++|+||+|++++++++++.. +-++|+++.|+|+.|.++....+..
T Consensus       119 e~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~-~f~~~~gk~vevkrA~pk~~~~~~~  183 (311)
T KOG4205|consen  119 EQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ-KFHDFNGKKVEVKRAIPKEVMQSTK  183 (311)
T ss_pred             hccceeEeeEEeecccccccccceeeEeccccccceeccc-ceeeecCceeeEeeccchhhccccc
Confidence            9999999999999999999999999999999999999987 7889999999999999998776543

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=4.7e-20  Score=157.34  Aligned_cols=133  Identities=29%  Similarity=0.567  Sum_probs=119.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+||.|+.|-||+||-|.+++||++|+...  ..+..|+|+|..+.|.    ++.++...|||..||..+|..||+++|+
T Consensus        74 vRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPS----s~~Ik~aNLYvSGlPktMtqkelE~iFs  149 (360)
T KOG0145|consen   74 VRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPS----SDSIKDANLYVSGLPKTMTQKELEQIFS  149 (360)
T ss_pred             eeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCC----hhhhcccceEEecCCccchHHHHHHHHH
Confidence            689999999999999999999999999943  4677888888887765    3456677899999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeecCCCC
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKAEPKK  137 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a~~~~  137 (314)
                      +||.|...+|+.|..|+.+||.+||.|+..++|++||+.||+..-.+  .+|.|++|....
T Consensus       150 ~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  150 PFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             HhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            99999999999999999999999999999999999999999987655  679999987653

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=1.2e-19  Score=168.59  Aligned_cols=138  Identities=22%  Similarity=0.429  Sum_probs=119.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC--------------------C--CCCc
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS--------------------K--DFKT   56 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~--------------------~--~~~~   56 (314)
                      ++++.+.++|||+||+|+-+++++.|++  ....+.++.|.|+.+..+.....                    .  +.+.
T Consensus        38 Vt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k  117 (678)
T KOG0127|consen   38 VTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPK  117 (678)
T ss_pred             ecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccccchhhhcccccCCcchhhccCcc
Confidence            4688899999999999999999999998  44469999999987665533221                    1  2235


Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      .+|+|.||||.|.+++|+.+|+.||.|.+|.|++.+ .++..|||||.|.+..+|++||+.+|...|.+|+|-|.||.++
T Consensus       118 ~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  118 WRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             ceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            689999999999999999999999999999999765 5566799999999999999999999999999999999999988


Q ss_pred             CCC
Q 021295          137 KPN  139 (314)
Q Consensus       137 ~~~  139 (314)
                      ...
T Consensus       197 d~y  199 (678)
T KOG0127|consen  197 DTY  199 (678)
T ss_pred             ccc
Confidence            654

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

Probab=99.81  E-value=1.9e-19  Score=174.90  Aligned_cols=126  Identities=25%  Similarity=0.481  Sum_probs=100.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccC--ccC-CcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IIN-GKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFF   77 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~--~i~-g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F   77 (314)
                      |+| .|+++||||||+|.+.++|++||+.++  +|. ++.|.|..+          ...++|||.|||+++++++|+++|
T Consensus        91 ~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S----------~~~~rLFVgNLP~~~TeeeL~eeF  159 (578)
T TIGR01648        91 MMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS----------VDNCRLFVGGIPKNKKREEILEEF  159 (578)
T ss_pred             EEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc----------ccCceeEeecCCcchhhHHHHHHh
Confidence            467 799999999999999999999999543  342 455554433          235789999999999999999999


Q ss_pred             hccCC-eEEEEEe-ecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEEEEeecCCCC
Q 021295           78 MQFGD-VQEHQIM-RDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        78 ~~~G~-v~~v~i~-~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l~V~~a~~~~  137 (314)
                      +++.+ |+++.|+ .+..+.++++||||+|+++++|++|+++|+  .+.|.++.|.|+++.++.
T Consensus       160 skv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       160 SKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             hcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccc
Confidence            99864 4444333 334456789999999999999999999875  467899999999988754

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.81  E-value=1.2e-19  Score=147.32  Aligned_cols=134  Identities=27%  Similarity=0.441  Sum_probs=118.3

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      +|+.|...+|||||||.++|+|+=|++  ++..+-+++|+|..+...   .+.......|||+||.++++|..|.+.|++
T Consensus        43 kDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~---~~nl~vganlfvgNLd~~vDe~~L~dtFsa  119 (203)
T KOG0131|consen   43 KDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAH---QKNLDVGANLFVGNLDPEVDEKLLYDTFSA  119 (203)
T ss_pred             hhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccc---cccccccccccccccCcchhHHHHHHHHHh
Confidence            578889999999999999999999998  666788999999987722   223334579999999999999999999999


Q ss_pred             cCCeEE-EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           80 FGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        80 ~G~v~~-v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      ||.|.. -+|+++..|+.+++|+||.|++.|++.+||+.+|+..++.++|.|..+..+..
T Consensus       120 fG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  120 FGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             ccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            998765 57899999999999999999999999999999999999999999999886643

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.80  E-value=7.8e-19  Score=163.30  Aligned_cols=134  Identities=28%  Similarity=0.518  Sum_probs=114.0

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC-------------------------------
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS-------------------------------   51 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~-------------------------------   51 (314)
                      ..++.+|||||+|.+..+|.+||+  +.+.|.+++|.|+|++++.....                               
T Consensus       153 ~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~  232 (678)
T KOG0127|consen  153 KDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDE  232 (678)
T ss_pred             CCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccch
Confidence            345555999999999999999999  77799999999999876521000                               


Q ss_pred             ----------C---------------------------------------------CCCcceEEEcCCCCCCCHHHHHHH
Q 021295           52 ----------K---------------------------------------------DFKTKKIFVGGIPSSVNEDEFKDF   76 (314)
Q Consensus        52 ----------~---------------------------------------------~~~~~~l~V~nLp~~~~e~~l~~~   76 (314)
                                +                                             ....++|||.|||+++||++|.++
T Consensus       233 Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~  312 (678)
T KOG0127|consen  233 EDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEH  312 (678)
T ss_pred             hcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHH
Confidence                      0                                             001158999999999999999999


Q ss_pred             HhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc-----CC-eeeCCeEEEEeecCCCCC
Q 021295           77 FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-----NK-LELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        77 F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l-----~~-~~~~gr~l~V~~a~~~~~  138 (314)
                      |++||+|+.+.|+.++.|++++|+|||.|.++.++.+||+..     .. +.|++|.|+|..|..++.
T Consensus       313 fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  313 FSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             HHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHH
Confidence            999999999999999999999999999999999999999975     23 779999999999887654

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

Probab=99.79  E-value=2.7e-18  Score=166.59  Aligned_cols=128  Identities=13%  Similarity=0.180  Sum_probs=106.3

Q ss_pred             CcccEEEEEECCHHHHHHHHHc----cCccCCcEEEEeecCCCCCCCC--------CCCCcceEEEcCCCCCCCHHHHHH
Q 021295            8 QPRGFGFVTYADPSVVDKVIED----THIINGKQVEIKRTIPKGAVGS--------KDFKTKKIFVGGIPSSVNEDEFKD   75 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~----~~~i~g~~i~v~~~~~~~~~~~--------~~~~~~~l~V~nLp~~~~e~~l~~   75 (314)
                      ++|+||||+|+++++|++||+.    ...|.++.|.|+++..++....        ......+|||.||++++++++|++
T Consensus        36 ~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~  115 (481)
T TIGR01649        36 PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQ  115 (481)
T ss_pred             CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHH
Confidence            4679999999999999999973    3578999999999865432211        112334799999999999999999


Q ss_pred             HHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeecCCCCCC
Q 021295           76 FFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKAEPKKPN  139 (314)
Q Consensus        76 ~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a~~~~~~  139 (314)
                      +|++||+|++|.|+++..    +++|||+|+++++|++|++.||+.+|.+  +.|+|++++.....
T Consensus       116 ~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~  177 (481)
T TIGR01649       116 IFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLN  177 (481)
T ss_pred             HHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCce
Confidence            999999999999987643    4689999999999999999999999965  58999999876543

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).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.78  E-value=1.3e-18  Score=154.87  Aligned_cols=139  Identities=24%  Similarity=0.493  Sum_probs=120.5

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCCCC-------CCCCcceEEEcCCCCCCCHHH
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAVGS-------KDFKTKKIFVGGIPSSVNEDE   72 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~~~-------~~~~~~~l~V~nLp~~~~e~~   72 (314)
                      ||+.|++.|+||||||+-+|.|+.|++.+  ..+.++.|+|.+.......+.       +...-++|||..+..+++|+|
T Consensus       147 WDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~D  226 (544)
T KOG0124|consen  147 WDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETD  226 (544)
T ss_pred             cccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHH
Confidence            89999999999999999999999999954  478899999886443322211       223457999999999999999


Q ss_pred             HHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCC
Q 021295           73 FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  140 (314)
Q Consensus        73 l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~  140 (314)
                      |+.+|+.||+|+.|.+.+++....+|||.||||++..+..+||..||-+++.++.|+|-.+......+
T Consensus       227 iKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aL  294 (544)
T KOG0124|consen  227 IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDAL  294 (544)
T ss_pred             HHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCchh
Confidence            99999999999999999999999999999999999999999999999999999999998876655433

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

Probab=99.78  E-value=4.6e-18  Score=164.99  Aligned_cols=126  Identities=15%  Similarity=0.294  Sum_probs=103.2

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC---------------------------------CC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS---------------------------------KD   53 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~---------------------------------~~   53 (314)
                      .|+||||+|++.++|++||+  +...|.++.|.|..+........                                 ..
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~  391 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQ  391 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccC
Confidence            47999999999999999998  45588999999987533210000                                 01


Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCC--eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE----
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGD--VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ----  127 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~--v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~----  127 (314)
                      .++++|||.|||++++|++|+++|++||.  |+.|+|+... + ..+++|||+|++.++|.+||..||...|.++.    
T Consensus       392 ~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~-~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~  469 (481)
T TIGR01649       392 PPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-N-ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAP  469 (481)
T ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-C-CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCcc
Confidence            24578999999999999999999999998  8888887653 2 25789999999999999999999999999885    


Q ss_pred             --EEEeecCCC
Q 021295          128 --VEVKKAEPK  136 (314)
Q Consensus       128 --l~V~~a~~~  136 (314)
                        |+|.+++++
T Consensus       470 ~~lkv~fs~~~  480 (481)
T TIGR01649       470 YHLKVSFSTSR  480 (481)
T ss_pred             ceEEEEeccCC
Confidence              999888764

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=99.77  E-value=6.1e-18  Score=165.53  Aligned_cols=135  Identities=19%  Similarity=0.273  Sum_probs=109.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC------------------------CCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG------------------------SKDF   54 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~------------------------~~~~   54 (314)
                      |+|+.|++++|||||+|.+.++|++||+  +...|.++.|.|+++.......                        ....
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  407 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGK  407 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCC
Confidence            4678899999999999999999999998  4468889999998864321110                        0123


Q ss_pred             CcceEEEcCCCCCC----------CHHHHHHHHhccCCeEEEEEeecC---CCCCcceEEEEEeCChHHHHHHHHhcCCe
Q 021295           55 KTKKIFVGGIPSSV----------NEDEFKDFFMQFGDVQEHQIMRDH---STSRSRGFGFITFDTEQAVDDLLAKGNKL  121 (314)
Q Consensus        55 ~~~~l~V~nLp~~~----------~e~~l~~~F~~~G~v~~v~i~~~~---~~g~~rG~afV~F~~~~~a~~a~~~l~~~  121 (314)
                      ++++|+|.||....          ..++|+++|++||.|+.|.|+++.   .+...+|+|||+|+++++|++||+.||+.
T Consensus       408 ~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       408 PTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             CceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC
Confidence            56789999996421          236799999999999999998752   34456899999999999999999999999


Q ss_pred             eeCCeEEEEeecCC
Q 021295          122 ELAGAQVEVKKAEP  135 (314)
Q Consensus       122 ~~~gr~l~V~~a~~  135 (314)
                      +|.++.|+|.+...
T Consensus       488 ~~~gr~v~~~~~~~  501 (509)
T TIGR01642       488 KFNDRVVVAAFYGE  501 (509)
T ss_pred             EECCeEEEEEEeCH
Confidence            99999999998764

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=99.74  E-value=2.3e-17  Score=153.50  Aligned_cols=122  Identities=22%  Similarity=0.541  Sum_probs=109.7

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      +|. |  |-|||||.|.++++|++||+  +-..+.+++|++.|+......         |||.||+.+++..+|.++|+.
T Consensus        32 ~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~~---------~~i~nl~~~~~~~~~~d~f~~   99 (369)
T KOG0123|consen   32 RDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPSL---------VFIKNLDESIDNKSLYDTFSE   99 (369)
T ss_pred             ecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCce---------eeecCCCcccCcHHHHHHHHh
Confidence            566 6  99999999999999999999  445899999999987654333         999999999999999999999


Q ss_pred             cCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           80 FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        80 ~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      ||+|..|+|.++.. + +++| ||+|+++++|++||++||+..+.+++|.|.....++.
T Consensus       100 ~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen  100 FGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             hcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            99999999999964 3 9999 9999999999999999999999999999987776654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.73  E-value=1.9e-17  Score=153.27  Aligned_cols=85  Identities=22%  Similarity=0.426  Sum_probs=80.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|||.+||+++||++|+++|++|++|++|+|++|+.++++++||||+|+++++|++||+.||+++|.+++|+|.
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            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            88764

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).

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.73  E-value=5.9e-18  Score=158.05  Aligned_cols=138  Identities=25%  Similarity=0.465  Sum_probs=118.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC--------C--CCCCCcceEEEcCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV--------G--SKDFKTKKIFVGGIPSSVN   69 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~--------~--~~~~~~~~l~V~nLp~~~~   69 (314)
                      |.|+.+.++||.|+|+|.|.+.+..||. ..+.+.+.+|.|+.+......        .  ....+...|||+||.++++
T Consensus       212 I~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNit  291 (549)
T KOG0147|consen  212 IGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNIT  291 (549)
T ss_pred             eccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCch
Confidence            6789999999999999999999999887 666788888888765432211        1  1122334599999999999


Q ss_pred             HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           70 EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        70 e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      |++|+.+|+.|+.|+.|.+++|.+|+++|+|+||+|.+.++|++|+++||+++|.++.|+|.....+..
T Consensus       292 e~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  292 EDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             HHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            999999999999999999999999999999999999999999999999999999999999987766543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=3.5e-17  Score=142.37  Aligned_cols=99  Identities=17%  Similarity=0.365  Sum_probs=88.2

Q ss_pred             CCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           44 IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        44 ~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      .|.........+-+||||.-|+++++|.+|+.+|++||+|+.|+|+.|..|++++|||||+|+++.++.+|.+..+++.|
T Consensus        89 dP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~I  168 (335)
T KOG0113|consen   89 DPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKI  168 (335)
T ss_pred             CCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCcee
Confidence            34444445567789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeEEEEeecCCCCCCCCC
Q 021295          124 AGAQVEVKKAEPKKPNLPQ  142 (314)
Q Consensus       124 ~gr~l~V~~a~~~~~~~~~  142 (314)
                      +++.|.|..........+.
T Consensus       169 dgrri~VDvERgRTvkgW~  187 (335)
T KOG0113|consen  169 DGRRILVDVERGRTVKGWL  187 (335)
T ss_pred             cCcEEEEEecccccccccc
Confidence            9999999887776655443

>PF00076 RRM_1: RNA recognition motif

Probab=99.69  E-value=2.2e-16  Score=112.10  Aligned_cols=70  Identities=33%  Similarity=0.805  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        59 l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      |||.|||+++++++|+++|++||+|+.+.|+.+ .+++++++|||+|+++++|++|++.|++..+.+++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 6788999999999999999999999999999999885

(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 ....

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.69  E-value=8.5e-17  Score=154.13  Aligned_cols=131  Identities=26%  Similarity=0.474  Sum_probs=113.6

Q ss_pred             CcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCCCCC-----CCCCCCcceEEEcCCCCCCCHHHHHHHHhcc
Q 021295            8 QPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPKGAV-----GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQF   80 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~~~~-----~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~   80 (314)
                      .|.||+||+|.++++|+.|+++  .+.|++..|.|+.+..+...     .......++|+|.|||+.++..+|+++|..|
T Consensus       558 lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aF  637 (725)
T KOG0110|consen  558 LSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAF  637 (725)
T ss_pred             cccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcc
Confidence            4669999999999999999995  46999999999987722211     1223335799999999999999999999999


Q ss_pred             CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           81 GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        81 G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      |+|+.|+|+.......++|||||+|.++++|..|+++|..+.|-+|.|.++||.....
T Consensus       638 GqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  638 GQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             cceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccchH
Confidence            9999999998766677899999999999999999999999999999999999987654

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=7.5e-16  Score=131.75  Aligned_cols=136  Identities=22%  Similarity=0.332  Sum_probs=112.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--C--ccCCcEEEEeecCCCCCCCC-------------------------
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--H--IINGKQVEIKRTIPKGAVGS-------------------------   51 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~--~i~g~~i~v~~~~~~~~~~~-------------------------   51 (314)
                      +.|..|+.+||-+||.|...++|++|++.+  +  .-...+|.|+.+........                         
T Consensus       160 L~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r  239 (360)
T KOG0145|consen  160 LVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQR  239 (360)
T ss_pred             hhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhh
Confidence            357789999999999999999999999833  2  22346677776532210000                         


Q ss_pred             ----------------------------------CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCc
Q 021295           52 ----------------------------------KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRS   97 (314)
Q Consensus        52 ----------------------------------~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~   97 (314)
                                                        ......+|||-||..+++|..|.++|..||.|..|+|++|..|.+.
T Consensus       240 ~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkC  319 (360)
T KOG0145|consen  240 FRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKC  319 (360)
T ss_pred             hccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccc
Confidence                                              0112248999999999999999999999999999999999999999


Q ss_pred             ceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           98 RGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        98 rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      |||+||++++-++|..||..||+..+.++.|.|.+...+
T Consensus       320 KGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  320 KGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             cceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            999999999999999999999999999999999987654

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.68  E-value=1.1e-16  Score=138.77  Aligned_cols=117  Identities=21%  Similarity=0.489  Sum_probs=106.4

Q ss_pred             ccEEEEEECCHHHHHHHHHccC--ccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEE
Q 021295           10 RGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQ   87 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~~~~--~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~   87 (314)
                      |=|+||..+|..+++.|+.+++  +|++..|.|+.++.+      ...+.+|+|+||.+.++.+||++.|++||+|++++
T Consensus        36 KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecd  109 (346)
T KOG0109|consen   36 KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECD  109 (346)
T ss_pred             cccceEEeecccccHHHHhhcccceecceEEEEEecccc------CCCccccccCCCCccccCHHHhhhhcccCCceeee
Confidence            5599999999999999999776  889999999987765      44578999999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCC
Q 021295           88 IMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  140 (314)
Q Consensus        88 i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~  140 (314)
                      |++|        |+||.|+-.++|..||+.|++.+|.+++|+|.....+....
T Consensus       110 ivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrta  154 (346)
T KOG0109|consen  110 IVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA  154 (346)
T ss_pred             eecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeeccccccC
Confidence            9977        99999999999999999999999999999999988765443

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

Probab=99.67  E-value=1.3e-15  Score=147.15  Aligned_cols=132  Identities=17%  Similarity=0.300  Sum_probs=106.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC-----------------------------
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV-----------------------------   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~-----------------------------   49 (314)
                      ++|+.|+++|+||||+|.+.++|++||+  +...|.++.|.|.++......                             
T Consensus       219 ~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  298 (457)
T TIGR01622       219 HRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLM  298 (457)
T ss_pred             EEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHH
Confidence            3577889999999999999999999998  445889999999884211000                             


Q ss_pred             -------------------------------------C------------------C--CCCCcceEEEcCCCCCCC---
Q 021295           50 -------------------------------------G------------------S--KDFKTKKIFVGGIPSSVN---   69 (314)
Q Consensus        50 -------------------------------------~------------------~--~~~~~~~l~V~nLp~~~~---   69 (314)
                                                           .                  .  ....+++|+|.||....+   
T Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~  378 (457)
T TIGR01622       299 EKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEE  378 (457)
T ss_pred             HhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCccccc
Confidence                                                 0                  0  113557889999965544   


Q ss_pred             -------HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           70 -------EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        70 -------e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                             ++||+++|++||+|++|.|+..    ...|++||+|+++++|++|++.||+..|+++.|.|.+....
T Consensus       379 ~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       379 PNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             chHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence                   3689999999999999999743    35799999999999999999999999999999999987654

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.

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.67  E-value=2.9e-16  Score=133.33  Aligned_cols=82  Identities=23%  Similarity=0.464  Sum_probs=79.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ++.+|-|.||+.+++|++|+++|.+||.|.+|.|.+|+.|+.+||||||+|++.++|.+||+.||++-++.-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            85

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.66  E-value=2e-16  Score=133.74  Aligned_cols=83  Identities=29%  Similarity=0.561  Sum_probs=76.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+..-++|||++|+|+++.|+|+++|++||+|+++.|+.|+.|+++|||+||+|.|.|+|++|++. .+-.|++|+..|+
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            345568999999999999999999999999999999999999999999999999999999999998 4557999999888


Q ss_pred             ecCC
Q 021295          132 KAEP  135 (314)
Q Consensus       132 ~a~~  135 (314)
                      +|.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            8765

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=2.4e-16  Score=121.13  Aligned_cols=83  Identities=17%  Similarity=0.298  Sum_probs=78.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .++++|||+||++.++||+|.++|+++|+|..|.|-.|+.+..+.|||||+|-+.++|+.|++-++++.|+.++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      .--
T Consensus       114 ~GF  116 (153)
T KOG0121|consen  114 AGF  116 (153)
T ss_pred             ccc
Confidence            543

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.64  E-value=6.6e-16  Score=136.07  Aligned_cols=83  Identities=25%  Similarity=0.496  Sum_probs=76.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|+|+|||+...|.||+.+|++||+|.+|+|+.+.  .-+|||.||+|+++++|++|-++||+..|.+|+|+|.
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn  169 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVN  169 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEe
Confidence            44567899999999999999999999999999999999873  3489999999999999999999999999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      .|+.+
T Consensus       170 ~ATar  174 (376)
T KOG0125|consen  170 NATAR  174 (376)
T ss_pred             ccchh
Confidence            98765

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.63  E-value=1e-15  Score=123.92  Aligned_cols=77  Identities=19%  Similarity=0.493  Sum_probs=72.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      -.++|||+||+..+++.||+.+|.+||+|..|+|.++     +.|||||||+++.+|+.|+..|++..|++..|.|++.+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            4689999999999999999999999999999999986     46899999999999999999999999999999999877


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      -+
T Consensus        84 G~   85 (195)
T KOG0107|consen   84 GR   85 (195)
T ss_pred             CC
Confidence            54

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.63  E-value=2.6e-15  Score=131.06  Aligned_cols=79  Identities=18%  Similarity=0.332  Sum_probs=72.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      .++|||+|||+.++|++|+++|+.||+|++|+|++++.   +++||||+|+++++|++||. |++..|.+++|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998864   47899999999999999995 899999999999999886


Q ss_pred             CCC
Q 021295          136 KKP  138 (314)
Q Consensus       136 ~~~  138 (314)
                      ...
T Consensus        80 ~~~   82 (260)
T PLN03120         80 YQL   82 (260)
T ss_pred             CCC
Confidence            543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.62  E-value=2.6e-15  Score=106.99  Aligned_cols=70  Identities=27%  Similarity=0.693  Sum_probs=65.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        59 l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      |||.|||+++++++|+++|+.++.|..|.++.+++ ++++++|||+|.++++|++|++.+++..|+++.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999976 88999999999999999999999999999999885

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.59  E-value=1.3e-15  Score=148.59  Aligned_cols=82  Identities=23%  Similarity=0.454  Sum_probs=77.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ...++|||+|||++++|++|+++|++||+|++|+|+.|+.+++++|||||+|+++++|++||+.||+..|.+++|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC
Q 021295          134 EP  135 (314)
Q Consensus       134 ~~  135 (314)
                      ..
T Consensus       185 ~~  186 (612)
T TIGR01645       185 SN  186 (612)
T ss_pred             cc
Confidence            43

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.

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.59  E-value=7e-15  Score=136.02  Aligned_cols=132  Identities=19%  Similarity=0.357  Sum_probs=107.2

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCC-------CCCCcceEEEcCCCCCCCHHHHH
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGS-------KDFKTKKIFVGGIPSSVNEDEFK   74 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~-------~~~~~~~l~V~nLp~~~~e~~l~   74 (314)
                      .+.|+++.|-|||||++++++++||+ +-..+..+.|+|-.+..++....       .......|-|..||+.|||+||.
T Consensus        42 ~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~  121 (510)
T KOG4211|consen   42 PRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIV  121 (510)
T ss_pred             eccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHH
Confidence            45689999999999999999999999 44577888899977755543222       12355689999999999999999


Q ss_pred             HHHhccCCeEE-EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           75 DFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        75 ~~F~~~G~v~~-v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      +||+-.-.|.. |.++.+ ..+++.+-|||.|++.+.|++||.+ |...|..+-|+|..+...
T Consensus       122 ~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss~~  182 (510)
T KOG4211|consen  122 EFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSSRA  182 (510)
T ss_pred             HHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhHHH
Confidence            99998866655 445555 4567999999999999999999999 888899999999766543

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.59  E-value=2.4e-15  Score=124.65  Aligned_cols=86  Identities=26%  Similarity=0.434  Sum_probs=81.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..-..+|.|.||.+-|+.++|+.+|++||.|.+|.|++|+.|.++++||||.|.+..+|++|+++|++.+|+++.|.|+.
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      |+-..+
T Consensus        90 arygr~   95 (256)
T KOG4207|consen   90 ARYGRP   95 (256)
T ss_pred             hhcCCC
Confidence            886654

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.58  E-value=7.3e-15  Score=126.45  Aligned_cols=101  Identities=20%  Similarity=0.493  Sum_probs=86.2

Q ss_pred             EEEEeecCCCCCCCCCCC-CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHH
Q 021295           37 QVEIKRTIPKGAVGSKDF-KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL  115 (314)
Q Consensus        37 ~i~v~~~~~~~~~~~~~~-~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~  115 (314)
                      .|+|.++......+.++. .-..|||+.|..+++.|+|++.|.+||+|.+++|++|..|.++|||+||.|.+.++|+.||
T Consensus        42 e~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI  121 (321)
T KOG0148|consen   42 ELKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAI  121 (321)
T ss_pred             hhccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHH
Confidence            344445544422222222 2457999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCeeeCCeEEEEeecCCCC
Q 021295          116 AKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus       116 ~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      +.||+.+|..|.|+..||..|.
T Consensus       122 ~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  122 QQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             HHhCCeeeccceeeccccccCc
Confidence            9999999999999999999876

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.56  E-value=1.1e-14  Score=112.99  Aligned_cols=88  Identities=23%  Similarity=0.429  Sum_probs=82.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ....-..|||.++..+++|++|.+.|..||+|+.|.|..|+.|+-.||||+|+|++.+.|++||+.||+.+|.+++|.|.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VD  147 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVD  147 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ||-.+.+.
T Consensus       148 w~Fv~gp~  155 (170)
T KOG0130|consen  148 WCFVKGPE  155 (170)
T ss_pred             EEEecCCc
Confidence            99876554

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.55  E-value=2.4e-14  Score=116.89  Aligned_cols=78  Identities=21%  Similarity=0.558  Sum_probs=70.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .+++|||+|||.++.|.||+++|.||+.|.+|+|...+   .+-.||||+|+++.+|+.||..-++..++++.|+|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            46899999999999999999999999999999986443   346699999999999999999999999999999999876


Q ss_pred             C
Q 021295          135 P  135 (314)
Q Consensus       135 ~  135 (314)
                      .
T Consensus        82 g   82 (241)
T KOG0105|consen   82 G   82 (241)
T ss_pred             C
Confidence            4

>PLN03213 repressor of silencing 3; Provisional

Probab=99.55  E-value=2e-14  Score=132.78  Aligned_cols=81  Identities=22%  Similarity=0.446  Sum_probs=74.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCCh--HHHHHHHHhcCCeeeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE--QAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~--~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ......+|||+||+++++++||+++|++||.|++|.|+  +.|+  |+||||+|.+.  +++++||+.||+..+.++.|+
T Consensus         6 s~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LK   81 (759)
T PLN03213          6 SGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLR   81 (759)
T ss_pred             cCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeE
Confidence            34456899999999999999999999999999999999  5566  99999999987  789999999999999999999


Q ss_pred             EeecCCC
Q 021295          130 VKKAEPK  136 (314)
Q Consensus       130 V~~a~~~  136 (314)
                      |..|++.
T Consensus        82 VNKAKP~   88 (759)
T PLN03213         82 LEKAKEH   88 (759)
T ss_pred             EeeccHH
Confidence            9988874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.54  E-value=4.9e-14  Score=121.22  Aligned_cols=80  Identities=15%  Similarity=0.237  Sum_probs=71.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ...+|||.||++.+||++|++||+.||+|++|+|++|..   .++||||+|+++++++.|| .|++..|.+++|+|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            457999999999999999999999999999999998853   4579999999999999999 569999999999999877


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      ....
T Consensus        80 ~y~~   83 (243)
T PLN03121         80 QYED   83 (243)
T ss_pred             cccc
Confidence            5543

>smart00362 RRM_2 RNA recognition motif

Probab=99.54  E-value=5.6e-14  Score=99.13  Aligned_cols=72  Identities=31%  Similarity=0.721  Sum_probs=67.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +|||.+||.++++++|+++|+++++|+.+.++.++  +.++++|||+|.++++|++|++.+++..+.+++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999999876  6788999999999999999999999999999999874

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=8e-16  Score=125.12  Aligned_cols=83  Identities=22%  Similarity=0.524  Sum_probs=77.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .++.-|||++||+++||.||..+|++||+|++|.|++|..|++++||||+.|++..+.--|+..||++.|.+|.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      ...
T Consensus       113 ~~Y  115 (219)
T KOG0126|consen  113 SNY  115 (219)
T ss_pred             ccc
Confidence            544

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=7.8e-15  Score=122.73  Aligned_cols=87  Identities=30%  Similarity=0.593  Sum_probs=82.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||+.|..+++|..|...|-.||.|++|.|+.|.++.++|+|+||||+..|+|.+||..||..+|.+|.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 021295          133 AEPKKPN  139 (314)
Q Consensus       133 a~~~~~~  139 (314)
                      |+|.+..
T Consensus        87 AkP~kik   93 (298)
T KOG0111|consen   87 AKPEKIK   93 (298)
T ss_pred             cCCcccc
Confidence            9987653

>smart00360 RRM RNA recognition motif

Probab=99.52  E-value=7.6e-14  Score=98.02  Aligned_cols=71  Identities=35%  Similarity=0.755  Sum_probs=67.1

Q ss_pred             EcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        61 V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      |.|||+++++++|+++|++||.|+.+.|+.++.+.+++++|||+|.+.++|++|++.+++..+.++.|.|+
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            57999999999999999999999999999988888999999999999999999999999999999998874

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=6e-14  Score=120.61  Aligned_cols=85  Identities=22%  Similarity=0.508  Sum_probs=80.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      -+.|||-.||.+..+.||.+.|..||.|++.+|..|+.|+++|.|.||.|+++.++++||..||++.|.=++|+|...++
T Consensus       285 GCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRP  364 (371)
T KOG0146|consen  285 GCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRP  364 (371)
T ss_pred             cceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCc
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             CCCCC
Q 021295          136 KKPNL  140 (314)
Q Consensus       136 ~~~~~  140 (314)
                      +..+.
T Consensus       365 kdanR  369 (371)
T KOG0146|consen  365 KDANR  369 (371)
T ss_pred             cccCC
Confidence            76543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.50  E-value=6.2e-14  Score=130.63  Aligned_cols=136  Identities=23%  Similarity=0.522  Sum_probs=114.3

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCC--------------CCCCCCcceEEEcCCCC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAV--------------GSKDFKTKKIFVGGIPS   66 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~--------------~~~~~~~~~l~V~nLp~   66 (314)
                      ...++++++|+||+|+++++|..|++.+  ..+..+.+.|..+..+...              .........|||.||+.
T Consensus       201 ~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~  280 (369)
T KOG0123|consen  201 RDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDE  280 (369)
T ss_pred             ecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCcc
Confidence            3457789999999999999999999944  4666677777766553111              11245667999999999


Q ss_pred             CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295           67 SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        67 ~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      .++++.|+++|+.+++|..++|+.+ ..+++++|+||+|+++++|.+|+..+|+..+.+++|.|.++..++..
T Consensus       281 ~~~~e~L~~~f~~~GeI~s~kv~~~-~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r  352 (369)
T KOG0123|consen  281 TLSDEKLRKIFSSFGEITSAKVMVD-ENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDR  352 (369)
T ss_pred             ccchhHHHHHHhcccceeeEEEEec-cCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccc
Confidence            9999999999999999999999998 57889999999999999999999999999999999999988855433

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.50  E-value=5.3e-14  Score=128.11  Aligned_cols=88  Identities=30%  Similarity=0.576  Sum_probs=79.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee-eCC--eEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE-LAG--AQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~-~~g--r~l  128 (314)
                      .+.+.-+|||+-||..++|.||+++|++||.|.+|.|++|+.|+.+++||||+|.+.++|.+|+.+||++. |.+  ++|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            44567799999999999999999999999999999999999999999999999999999999999997754 444  889


Q ss_pred             EEeecCCCCCC
Q 021295          129 EVKKAEPKKPN  139 (314)
Q Consensus       129 ~V~~a~~~~~~  139 (314)
                      .|++|..++++
T Consensus       110 qvk~Ad~E~er  120 (510)
T KOG0144|consen  110 QVKYADGERER  120 (510)
T ss_pred             eecccchhhhc
Confidence            99998877654

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.49  E-value=1.9e-13  Score=101.37  Aligned_cols=82  Identities=15%  Similarity=0.322  Sum_probs=74.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ..+.++.|||.|||+++|.|++.++|.+||.|..|+|-.+++|   +|.|||.|++..+|++|++.|++..++++.|.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            4456789999999999999999999999999999999877654   8999999999999999999999999999999998


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      +..+.
T Consensus        91 yyq~~   95 (124)
T KOG0114|consen   91 YYQPE   95 (124)
T ss_pred             ecCHH
Confidence            76554

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.49  E-value=6.9e-14  Score=127.47  Aligned_cols=81  Identities=25%  Similarity=0.494  Sum_probs=74.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHH-hccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFF-MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F-~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ..+.+||.|||+++.|++||++| ++.|+|+.|.|+.| .++|+|+||+|||+++|.+++|+++||++++.+|+|+|+..
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            34569999999999999999999 56799999999999 58999999999999999999999999999999999999876


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      ...
T Consensus       122 ~d~  124 (608)
T KOG4212|consen  122 HDE  124 (608)
T ss_pred             Cch
Confidence            653

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.48  E-value=4.8e-14  Score=114.92  Aligned_cols=85  Identities=28%  Similarity=0.503  Sum_probs=80.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+..+|||+||+..++++.|.++|-+.++|++|+|++|+.+.+.+|||||||.++|+|+-||+.||.+.|-+++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      ...+.
T Consensus        87 s~~~~   91 (203)
T KOG0131|consen   87 SAHQK   91 (203)
T ss_pred             ccccc
Confidence            84443

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

Probab=99.48  E-value=3.5e-13  Score=119.73  Aligned_cols=80  Identities=35%  Similarity=0.767  Sum_probs=77.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ..+|||+|||+++++++|+++|.+|+.|..|.|+.++.++++++||||+|.++++|..|++.++...|.+++|.|.++..
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            59999999999999999999999999999999999999999999999999999999999999999999999999999653

>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=99.47  E-value=5.6e-13  Score=94.44  Aligned_cols=74  Identities=35%  Similarity=0.740  Sum_probs=69.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      +|+|.+||.++++++|+++|+.+++|+.+.++.++.+ +++++|||+|.++++|+.|++.++...+.++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999988655 7789999999999999999999999999999998863

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=99.43  E-value=2.9e-13  Score=127.45  Aligned_cols=82  Identities=28%  Similarity=0.539  Sum_probs=79.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|||+|||++++|++|.++|++.+.|..++++.|++|+++|||+|++|++++++++|++.||..++.+++|+|.++...
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            89999999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             CC
Q 021295          137 KP  138 (314)
Q Consensus       137 ~~  138 (314)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            54

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=4.1e-12  Score=103.92  Aligned_cols=113  Identities=19%  Similarity=0.313  Sum_probs=93.3

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC----------------------CCCCCcceEEE
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG----------------------SKDFKTKKIFV   61 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~----------------------~~~~~~~~l~V   61 (314)
                      --..-.||||+|+++.+|+.||.  +...+++..|.|+.+..-....                      .......+|.|
T Consensus        41 r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvV  120 (241)
T KOG0105|consen   41 RPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVV  120 (241)
T ss_pred             CCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEE
Confidence            33456799999999999999998  7778999999998764332111                      12234568999


Q ss_pred             cCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           62 GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        62 ~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ..||.+.+|+|||+++.+.|+|+...|.+|-       +..|+|...|+++-||.+|+...+..
T Consensus       121 sGLp~SgSWQDLKDHmReaGdvCfadv~rDg-------~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  121 SGLPPSGSWQDLKDHMREAGDVCFADVQRDG-------VGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             ecCCCCCchHHHHHHHHhhCCeeeeeeeccc-------ceeeeeeehhhHHHHHHhhccccccC
Confidence            9999999999999999999999999998873       78999999999999999987766544

>smart00361 RRM_1 RNA recognition motif

Probab=99.37  E-value=3.5e-12  Score=90.95  Aligned_cols=62  Identities=24%  Similarity=0.418  Sum_probs=56.2

Q ss_pred             HHHHHHHHh----ccCCeEEEE-EeecCCC--CCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           70 EDEFKDFFM----QFGDVQEHQ-IMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        70 e~~l~~~F~----~~G~v~~v~-i~~~~~~--g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +++|+++|+    +||+|.+|. |+.++.+  ++++||+||+|+++++|++|++.||+..+.+++|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            678888888    999999996 7777666  8899999999999999999999999999999999873

>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=1.5e-12  Score=113.37  Aligned_cols=74  Identities=27%  Similarity=0.636  Sum_probs=70.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      .+|||+|||.++++.+|+.+|++|++|.+++|+++        |+||..++..+++.||..||...|++..|.|+.++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            57999999999999999999999999999999977        9999999999999999999999999999999998887


Q ss_pred             CC
Q 021295          137 KP  138 (314)
Q Consensus       137 ~~  138 (314)
                      ..
T Consensus        75 sk   76 (346)
T KOG0109|consen   75 SK   76 (346)
T ss_pred             CC
Confidence            43

>PF13893 RRM_5: RNA recognition motif

Probab=99.31  E-value=9.9e-12  Score=84.50  Aligned_cols=56  Identities=25%  Similarity=0.559  Sum_probs=51.0

Q ss_pred             HHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           73 FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        73 l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      |+++|++||+|++|.+..+.     +++|||+|++.++|++|++.||+..+.+++|+|++|
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            78999999999999998763     579999999999999999999999999999999875

(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 ....

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.31  E-value=3.4e-12  Score=113.76  Aligned_cols=84  Identities=17%  Similarity=0.389  Sum_probs=79.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      .++.+.|||..|.+-++++||.-+|+.||+|+.+.|++|+.|+.+--||||||++.+++++|.-+|+++.|+.+.|.|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCCC
Q 021295          133 AEPK  136 (314)
Q Consensus       133 a~~~  136 (314)
                      ....
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            6654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.29  E-value=2.9e-11  Score=102.37  Aligned_cols=125  Identities=18%  Similarity=0.330  Sum_probs=101.7

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCCC--------------------------------
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAVG--------------------------------   50 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~~--------------------------------   50 (314)
                      .|.+.||-|||.|.+.+.|..|+.++  ..+-++.+++..+..+.+.-                                
T Consensus        47 kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~  126 (221)
T KOG4206|consen   47 KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHF  126 (221)
T ss_pred             CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccc
Confidence            58899999999999999999999844  36677777776654331110                                


Q ss_pred             --------------CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHH
Q 021295           51 --------------SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA  116 (314)
Q Consensus        51 --------------~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~  116 (314)
                                    ....+...||+.|||.+++.+.|..+|++|.-.++|+++..+     ++.|||+|++...+..|..
T Consensus       127 ~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~  201 (221)
T KOG4206|consen  127 YNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQ  201 (221)
T ss_pred             cccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhh
Confidence                          113456789999999999999999999999999999998764     5699999999999999999


Q ss_pred             hcCCeeeC-CeEEEEeecC
Q 021295          117 KGNKLELA-GAQVEVKKAE  134 (314)
Q Consensus       117 ~l~~~~~~-gr~l~V~~a~  134 (314)
                      .+....|. .+++.|.+++
T Consensus       202 ~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  202 ALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hhccceeccCceEEecccC
Confidence            99888876 7788887764

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.29  E-value=2.4e-12  Score=109.73  Aligned_cols=116  Identities=24%  Similarity=0.431  Sum_probs=93.3

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC------CC-------CC---CCCCCcceEEEcCCCCCCCH
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK------GA-------VG---SKDFKTKKIFVGGIPSSVNE   70 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~------~~-------~~---~~~~~~~~l~V~nLp~~~~e   70 (314)
                      -.+|+||+|.++.+|+.|+.  +..+|.+..+.++++...      ..       ..   ........|+|.+|+..+.|
T Consensus        34 k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~  113 (216)
T KOG0106|consen   34 KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSW  113 (216)
T ss_pred             ecccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhH
Confidence            45899999999999999998  344677777777776632      00       11   12345678999999999999


Q ss_pred             HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           71 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        71 ~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ++|+++|.++|++..+.+.        +.++||+|++.++|.+||++|+...|.++.|.+..
T Consensus       114 qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  114 QDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             HHHhhhhcccCCCchhhhh--------ccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            9999999999999655552        34899999999999999999999999999999943

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.25  E-value=7e-12  Score=113.38  Aligned_cols=83  Identities=41%  Similarity=0.772  Sum_probs=78.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +..+|||++|+|+++||.|++.|.+|++|.++.|++|+.++++++|.||+|++++.+.++|.. ..+.|+++.|+++.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678999999999999999999999999999999999999999999999999999999999887 6778999999999998


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      ++..
T Consensus        84 ~r~~   87 (311)
T KOG4205|consen   84 SRED   87 (311)
T ss_pred             Cccc
Confidence            8764

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=6.3e-12  Score=112.50  Aligned_cols=79  Identities=24%  Similarity=0.494  Sum_probs=75.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .++|||+.|.+++.|+.|+..|..||+|++|.+..|+.|+++|+||||||+-+|.|+-|++.||...+.+|.|+|....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            4689999999999999999999999999999999999999999999999999999999999999999999999997433

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.21  E-value=6.7e-11  Score=111.23  Aligned_cols=130  Identities=17%  Similarity=0.293  Sum_probs=97.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC----------------------------
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG----------------------------   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~----------------------------   50 (314)
                      ++|.+|+++|||+||+|.+.++|.+|++  +..+|.++.|+|...+.+....                            
T Consensus       311 ~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~  390 (549)
T KOG0147|consen  311 TKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLM  390 (549)
T ss_pred             ccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHH
Confidence            4677899999999999999999999988  4458889988874322110000                            


Q ss_pred             ----------------------------------------CCC-------CCcceEEEcCCCCCCCH----------HHH
Q 021295           51 ----------------------------------------SKD-------FKTKKIFVGGIPSSVNE----------DEF   73 (314)
Q Consensus        51 ----------------------------------------~~~-------~~~~~l~V~nLp~~~~e----------~~l   73 (314)
                                                              .+.       +++.+|.|.|+-...+|          |||
T Consensus       391 ~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV  470 (549)
T KOG0147|consen  391 AKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDV  470 (549)
T ss_pred             HHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHH
Confidence                                                    001       33445556665333222          677


Q ss_pred             HHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           74 KDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        74 ~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ++.+.++|+|..|.|-++     +.|+.||.|++.++|.+|+.+||+-||.++.|.+++...
T Consensus       471 ~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~  527 (549)
T KOG0147|consen  471 IEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPL  527 (549)
T ss_pred             HHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeeh
Confidence            788899999988877544     348999999999999999999999999999999987544

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.19  E-value=4.2e-11  Score=106.75  Aligned_cols=81  Identities=31%  Similarity=0.622  Sum_probs=72.4

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHh-cCCeeeCCeEE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK-GNKLELAGAQV  128 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~-l~~~~~~gr~l  128 (314)
                      +.++...++|||++|-..++|.+|+++|.+||+|+.|.|+..      +++|||+|++.++|+.|.++ ++.+.|+++.|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            345667789999999999999999999999999999999875      45999999999999999886 58888999999


Q ss_pred             EEeecCCC
Q 021295          129 EVKKAEPK  136 (314)
Q Consensus       129 ~V~~a~~~  136 (314)
                      +|.|..++
T Consensus       296 ~i~Wg~~~  303 (377)
T KOG0153|consen  296 KIKWGRPK  303 (377)
T ss_pred             EEEeCCCc
Confidence            99999883

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.19  E-value=6.8e-11  Score=98.60  Aligned_cols=85  Identities=25%  Similarity=0.444  Sum_probs=78.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhcc-CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQF-GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~-G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .......++|..||.-+.|.+|..+|.++ |.|.++++.+++.|+.+|+||||+|++++.|+-|.+.||+..|.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            44556789999999999999999999988 78888999999999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 021295          131 KKAEPK  136 (314)
Q Consensus       131 ~~a~~~  136 (314)
                      ....+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            877665

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=8.5e-11  Score=113.40  Aligned_cols=77  Identities=26%  Similarity=0.457  Sum_probs=69.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCC---CcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g---~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +|||.||+++++.++|.++|.+.|.|..|.|...+..-   .+.||+||+|.++++|++|+++|+.+.|+++.|+|+.+.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            49999999999999999999999999999888664321   245999999999999999999999999999999999988

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.18  E-value=2.3e-10  Score=107.29  Aligned_cols=79  Identities=28%  Similarity=0.577  Sum_probs=68.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      .+|||.|||.++++++|+++|.+||+|++..|.......+...|+||+|++.++++.||++ +.+.|.+++|.|+..++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            4699999999999999999999999999988876543344458999999999999999999 689999999999876543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.16  E-value=7.1e-11  Score=114.73  Aligned_cols=79  Identities=28%  Similarity=0.556  Sum_probs=73.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +.++||||+.|+..++|+||..+|++||+|++|.|+..      ++||||++....+|++||.+|+++.+..+.|+|.||
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            45689999999999999999999999999999999865      679999999999999999999999999999999999


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      ..+-.
T Consensus       493 ~g~G~  497 (894)
T KOG0132|consen  493 VGKGP  497 (894)
T ss_pred             ccCCc
Confidence            87654

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.15  E-value=5.8e-10  Score=102.18  Aligned_cols=127  Identities=24%  Similarity=0.393  Sum_probs=102.8

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC----------------------------------
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA----------------------------------   48 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~----------------------------------   48 (314)
                      +++++||+|.|||+++|.++||++  +.+++++++|.||.....+.                                  
T Consensus        81 ~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~gg  160 (608)
T KOG4212|consen   81 ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGG  160 (608)
T ss_pred             cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCC
Confidence            689999999999999999999999  55689999999975432100                                  


Q ss_pred             --------CCC---------------------------------------CCCCcceEEEcCCCCCCCHHHHHHHHhccC
Q 021295           49 --------VGS---------------------------------------KDFKTKKIFVGGIPSSVNEDEFKDFFMQFG   81 (314)
Q Consensus        49 --------~~~---------------------------------------~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G   81 (314)
                              ..+                                       ..+...++||.||.+.+..+.|++.|.-.|
T Consensus       161 G~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAG  240 (608)
T KOG4212|consen  161 GDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAG  240 (608)
T ss_pred             ccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccce
Confidence                    000                                       011224789999999999999999999999


Q ss_pred             CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           82 DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        82 ~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      +|+.|.+-.|++ +.+++||.|+++.+-+|-+||.+|+..-+..++..+..
T Consensus       241 kv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  241 KVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             eeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhccCCCccccceeec
Confidence            999999999965 58999999999999999999999987666666655554

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.14  E-value=1.6e-10  Score=97.79  Aligned_cols=83  Identities=19%  Similarity=0.440  Sum_probs=75.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHH----HHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           55 KTKKIFVGGIPSSVNEDEFKD----FFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~----~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      +..||||.||++.+..++|+.    +|++||+|.+|.++.   |.+.+|-|||.|++.++|..|+.+|+++.+-+++++|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            344999999999999999998    999999999998874   5678999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      .+|+.+....
T Consensus        85 qyA~s~sdii   94 (221)
T KOG4206|consen   85 QYAKSDSDII   94 (221)
T ss_pred             ecccCccchh
Confidence            9998876543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.11  E-value=2.6e-11  Score=109.17  Aligned_cols=132  Identities=17%  Similarity=0.269  Sum_probs=102.1

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHc-cCccCCcEEEEeecCCCCC---------------------------CCCCCCCc
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKGA---------------------------VGSKDFKT   56 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~~-~~~i~g~~i~v~~~~~~~~---------------------------~~~~~~~~   56 (314)
                      -+++..|-|||.|..+++|++||.+ ...|..+.|++-+++..+.                           ........
T Consensus       201 pdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~k  280 (508)
T KOG1365|consen  201 PDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSK  280 (508)
T ss_pred             CCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCC
Confidence            4789999999999999999999983 3345555555543321100                           00122346


Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCC-eEE--EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGD-VQE--HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~--v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+|.+.+||++++.|||.+||..|-. |..  |+|+.+ ..+++.|-|||+|.++|+|.+|..+.++..+..|.|+|..+
T Consensus       281 dcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  281 DCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            78999999999999999999998853 433  777777 57899999999999999999999999999999999999876


Q ss_pred             CCCC
Q 021295          134 EPKK  137 (314)
Q Consensus       134 ~~~~  137 (314)
                      ...+
T Consensus       360 S~ee  363 (508)
T KOG1365|consen  360 SVEE  363 (508)
T ss_pred             cHHH
Confidence            6544

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=1.3e-10  Score=110.25  Aligned_cols=132  Identities=24%  Similarity=0.454  Sum_probs=110.3

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCC-------------------CCCCCCCcceEEEcCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGA-------------------VGSKDFKTKKIFVGGIP   65 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~-------------------~~~~~~~~~~l~V~nLp   65 (314)
                      ..+.+-||||+|.+.++|.+|+. +...+.+.++++........                   .........+|||++||
T Consensus       219 ~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp  298 (500)
T KOG0120|consen  219 LNLEKNFAFIEFRSISEATEAMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLP  298 (500)
T ss_pred             ecccccceeEEecCCCchhhhhcccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCc
Confidence            45678899999999999999998 44456677776654322111                   11123456789999999


Q ss_pred             CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           66 SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        66 ~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      ..+++++++++++.|++++...++.|..++.+++|||.+|.++.....|++.||++.+.+++|.|..|....
T Consensus       299 ~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  299 LYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             CccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            999999999999999999999999999999999999999999999999999999999999999998877654

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=1.6e-10  Score=99.76  Aligned_cols=84  Identities=23%  Similarity=0.451  Sum_probs=75.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee-C--CeEEEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL-A--GAQVEV  130 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~-~--gr~l~V  130 (314)
                      .+.++|||+-|...-+|||++.+|..||+|+++.+++.. ++.+||||||.|.+..+|++||..||+... -  ...|.|
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVV   95 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVV   95 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEE
Confidence            367899999999999999999999999999999999884 688999999999999999999999988653 3  367999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      ++|...++
T Consensus        96 K~ADTdkE  103 (371)
T KOG0146|consen   96 KFADTDKE  103 (371)
T ss_pred             EeccchHH
Confidence            99887665

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.05  E-value=6.5e-10  Score=103.41  Aligned_cols=82  Identities=26%  Similarity=0.443  Sum_probs=70.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +......|-|..|||++|++||.+||+.+. |+.+.+.+  .++++.|-|||||+++|++++||++ +...|..+-|+|-
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEE
Confidence            344567889999999999999999999984 77766554  5899999999999999999999998 7888999999998


Q ss_pred             ecCCCC
Q 021295          132 KAEPKK  137 (314)
Q Consensus       132 ~a~~~~  137 (314)
                      .+...+
T Consensus        82 ~~~~~e   87 (510)
T KOG4211|consen   82 TAGGAE   87 (510)
T ss_pred             ccCCcc
Confidence            775543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.05  E-value=1.6e-09  Score=91.31  Aligned_cols=63  Identities=16%  Similarity=0.285  Sum_probs=50.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      .+|||.||..+|+|++|+.+|+.|--...++|...  .  .--.|||+|++.+.|..|+..|++..|
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~--g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--G--GMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--C--CcceEeecHHHHHHHHHHHHHhhccee
Confidence            38999999999999999999999976666666432  1  123799999999999999988877654

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.04  E-value=9.1e-10  Score=96.04  Aligned_cols=85  Identities=20%  Similarity=0.427  Sum_probs=77.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      +..+.+|+|.|||+.++++||+++|++|++++.+.|..++ .+++.|+|-|.|+..++|++|++.+|++.+++++|++..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445789999999999999999999999999999999984 788999999999999999999999999999999999988


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      ..+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            776544

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.03  E-value=5.2e-10  Score=105.37  Aligned_cols=81  Identities=22%  Similarity=0.521  Sum_probs=76.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      .+.|||..|+..+...||+.+|++||+|+-.+|+++..+.-.+.|.||++.+.++|.+||+.||.++|.++.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            46899999999999999999999999999999999988888899999999999999999999999999999999987765


Q ss_pred             C
Q 021295          136 K  136 (314)
Q Consensus       136 ~  136 (314)
                      .
T Consensus       485 E  485 (940)
T KOG4661|consen  485 E  485 (940)
T ss_pred             C
Confidence            3

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.03  E-value=2.9e-10  Score=97.57  Aligned_cols=131  Identities=21%  Similarity=0.331  Sum_probs=104.1

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC--CCCCCCCcceEEEcCCCCCCCHHHHHHHHhccC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA--VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFG   81 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~--~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G   81 (314)
                      -..-+.++|+.|....+..++..  +...+....|++-..+..++  ..+.+....+||++.|..+++++.|...|.+|-
T Consensus       136 p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfp  215 (290)
T KOG0226|consen  136 PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFP  215 (290)
T ss_pred             CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecccccccccHHHHHHHHHhcc
Confidence            34557889999988887777766  22344444455544333332  223556678999999999999999999999998


Q ss_pred             CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           82 DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        82 ~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      .....++++|+.|+++++|.||.|.+++++..|+..|++.-+..++|++....-+
T Consensus       216 sf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wk  270 (290)
T KOG0226|consen  216 SFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWK  270 (290)
T ss_pred             chhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHH
Confidence            8889999999999999999999999999999999999999999999988655443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=99.01  E-value=7.5e-10  Score=96.70  Aligned_cols=85  Identities=18%  Similarity=0.386  Sum_probs=79.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .++.+.+.|||+||.+.++.++|+.+|+.|+.|..|.|++|+.++++|+||||+|++.+.++++++ |+..+|.++.|+|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            467788999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             eecCCC
Q 021295          131 KKAEPK  136 (314)
Q Consensus       131 ~~a~~~  136 (314)
                      .+..-.
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            877665

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.96  E-value=3.8e-09  Score=100.51  Aligned_cols=135  Identities=21%  Similarity=0.369  Sum_probs=94.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCCC--------------------CCCCCcce
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAVG--------------------SKDFKTKK   58 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~~--------------------~~~~~~~~   58 (314)
                      ++|..|+.+|+|||.+|.++.....|+..+  ..+..+.+.|..+.+-....                    ..-.++..
T Consensus       322 v~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~V  401 (500)
T KOG0120|consen  322 VKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEV  401 (500)
T ss_pred             ecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchh
Confidence            467789999999999999999999888843  35566777776654321110                    11223334


Q ss_pred             EEEcCCC--CCC-CH-------HHHHHHHhccCCeEEEEEeecCCC---CCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           59 IFVGGIP--SSV-NE-------DEFKDFFMQFGDVQEHQIMRDHST---SRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        59 l~V~nLp--~~~-~e-------~~l~~~F~~~G~v~~v~i~~~~~~---g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      |.+.|+=  .++ ++       |+|++.+.+|+.|..|.|+++..+   .-..|..||||.+.+++++|.+.|++..|.+
T Consensus       402 l~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~n  481 (500)
T KOG0120|consen  402 LCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFAN  481 (500)
T ss_pred             hhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCC
Confidence            4444421  111 22       445566678999999999987222   2245779999999999999999999999999


Q ss_pred             eEEEEeecCC
Q 021295          126 AQVEVKKAEP  135 (314)
Q Consensus       126 r~l~V~~a~~  135 (314)
                      +.|...+-.+
T Consensus       482 RtVvtsYyde  491 (500)
T KOG0120|consen  482 RTVVASYYDE  491 (500)
T ss_pred             cEEEEEecCH
Confidence            9999887554

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.96  E-value=1.1e-08  Score=91.42  Aligned_cols=128  Identities=17%  Similarity=0.299  Sum_probs=100.5

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC---------C-------------------------CC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK---------G-------------------------AV   49 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~---------~-------------------------~~   49 (314)
                      .|+.||-|++.|...++++.|++  +...+.++.|+|+++.-.         .                         ..
T Consensus       179 ~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~  258 (382)
T KOG1548|consen  179 QGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDD  258 (382)
T ss_pred             CCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccc
Confidence            48899999999999999999998  666889999999765311         0                         00


Q ss_pred             CCCCCCcceEEEcCCCCC----CC-------HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc
Q 021295           50 GSKDFKTKKIFVGGIPSS----VN-------EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG  118 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~----~~-------e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l  118 (314)
                      .++....++|.|.||-.-    .+       +++|++..++||.|..|.|...+    +.|.+.|.|.+.++|+.||+.|
T Consensus       259 ~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~h----PdGvvtV~f~n~eeA~~ciq~m  334 (382)
T KOG1548|consen  259 PSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRH----PDGVVTVSFRNNEEADQCIQTM  334 (382)
T ss_pred             cccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccC----CCceeEEEeCChHHHHHHHHHh
Confidence            112334578999987532    23       35667778999999999887543    6789999999999999999999


Q ss_pred             CCeeeCCeEEEEeecCCCC
Q 021295          119 NKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus       119 ~~~~~~gr~l~V~~a~~~~  137 (314)
                      ++..|.+|+|..+....+.
T Consensus       335 ~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  335 DGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             cCeeecceEEEEEEeCCcc
Confidence            9999999999988765543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.88  E-value=1e-08  Score=91.71  Aligned_cols=83  Identities=19%  Similarity=0.381  Sum_probs=74.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA  124 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~--------~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~  124 (314)
                      ....+.|||.+||.++|.+++.++|++||.|.        .|+|.++. .++.||=|.|.|...++++-||+.|+...|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            34556799999999999999999999999876        48888885 5999999999999999999999999999999


Q ss_pred             CeEEEEeecCCC
Q 021295          125 GAQVEVKKAEPK  136 (314)
Q Consensus       125 gr~l~V~~a~~~  136 (314)
                      ++.|+|+.|+-.
T Consensus       210 g~~~rVerAkfq  221 (382)
T KOG1548|consen  210 GKKLRVERAKFQ  221 (382)
T ss_pred             CcEEEEehhhhh
Confidence            999999988654

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.87  E-value=8.4e-10  Score=92.78  Aligned_cols=79  Identities=19%  Similarity=0.251  Sum_probs=71.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +..++|||.||...++|+.|.++|-+.|+|.+|.|..++ +.+.| ||||+|+++.++.-|++.+|++.+.+++|.|++-
T Consensus         7 e~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    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            456899999999999999999999999999999999885 45566 9999999999999999999999999999888754


Q ss_pred             C
Q 021295          134 E  134 (314)
Q Consensus       134 ~  134 (314)
                      .
T Consensus        85 ~   85 (267)
T KOG4454|consen   85 C   85 (267)
T ss_pred             c
Confidence            3

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.87  E-value=1.9e-08  Score=90.73  Aligned_cols=127  Identities=13%  Similarity=0.176  Sum_probs=96.6

Q ss_pred             ccEEEEEECCHHHHHHHHH----ccCccCCcEEEEeecCCCCCCCC---CCCCcceE--EEcCCCCCCCHHHHHHHHhcc
Q 021295           10 RGFGFVTYADPSVVDKVIE----DTHIINGKQVEIKRTIPKGAVGS---KDFKTKKI--FVGGIPSSVNEDEFKDFFMQF   80 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~----~~~~i~g~~i~v~~~~~~~~~~~---~~~~~~~l--~V~nLp~~~~e~~l~~~F~~~   80 (314)
                      +-.|+|+|+|.+.|+.++.    +...|.++...+..++.+.....   .....+.|  .|-|--+.+|.|.|.++....
T Consensus        67 ~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~  146 (494)
T KOG1456|consen   67 KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQ  146 (494)
T ss_pred             cceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCC
Confidence            4468999999999998886    33466777777776654432221   11222333  446666789999999999999


Q ss_pred             CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeecCCCCCCCC
Q 021295           81 GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKAEPKKPNLP  141 (314)
Q Consensus        81 G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a~~~~~~~~  141 (314)
                      |+|.+|.|++.  +   --.|.|||++.++|++|.+.||+.+|..  ..|+|++|++.+.+..
T Consensus       147 GkVlRIvIfkk--n---gVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~  204 (494)
T KOG1456|consen  147 GKVLRIVIFKK--N---GVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQ  204 (494)
T ss_pred             CceEEEEEEec--c---ceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeee
Confidence            99999999875  2   3479999999999999999999999865  7899999999876543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.85  E-value=4.5e-09  Score=94.83  Aligned_cols=133  Identities=20%  Similarity=0.381  Sum_probs=104.2

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCC------CCCCCCcceEE-EcCCCCCCCHHHHH
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAV------GSKDFKTKKIF-VGGIPSSVNEDEFK   74 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~------~~~~~~~~~l~-V~nLp~~~~e~~l~   74 (314)
                      ...-.+++++.|.|+..+++..|++..  ..+....+...........      ........++| |.+|++++++++|+
T Consensus       124 ~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~  203 (285)
T KOG4210|consen  124 EDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLK  203 (285)
T ss_pred             ccccccccceeeccccHHHHHHHHHhhhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHh
Confidence            356789999999999999999999822  2334444443333222211      11233445566 99999999999999


Q ss_pred             HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           75 DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        75 ~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      ++|..+++|..|+++.++.++..++||+|+|.+...+..++.. +...+..++|.|....+..
T Consensus       204 ~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  204 EHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             hhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            9999999999999999999999999999999999999999987 7788889999988777653

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.83  E-value=1.1e-08  Score=92.14  Aligned_cols=87  Identities=25%  Similarity=0.406  Sum_probs=80.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA  124 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~--------~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~  124 (314)
                      .....+|||-.||..+++++|.++|.+++.|+        .|+|.+|++|.++|+-|.|+|+++.+|++||+.++...|+
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            45567999999999999999999999999886        4889999999999999999999999999999999999999


Q ss_pred             CeEEEEeecCCCCCC
Q 021295          125 GAQVEVKKAEPKKPN  139 (314)
Q Consensus       125 gr~l~V~~a~~~~~~  139 (314)
                      +.+|+|.+|..+...
T Consensus       143 gn~ikvs~a~~r~~v  157 (351)
T KOG1995|consen  143 GNTIKVSLAERRTGV  157 (351)
T ss_pred             CCCchhhhhhhccCc
Confidence            999999999877653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.77  E-value=8.1e-08  Score=87.70  Aligned_cols=121  Identities=14%  Similarity=0.224  Sum_probs=93.3

Q ss_pred             cEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC------CCCC-------------------------CCCCcc
Q 021295           11 GFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG------AVGS-------------------------KDFKTK   57 (314)
Q Consensus        11 G~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~------~~~~-------------------------~~~~~~   57 (314)
                      =-|+|+++|..+|+.|++  +.+.+.++.|+|..+....      ..++                         --+++.
T Consensus       336 d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~Ppsa  415 (492)
T KOG1190|consen  336 DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSA  415 (492)
T ss_pred             cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCCchh
Confidence            359999999999999999  6678889999997654221      1111                         013556


Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC-eEEEEeecCC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG-AQVEVKKAEP  135 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g-r~l~V~~a~~  135 (314)
                      +|.+.|+|.+++||+|+++|.+-|-++.......    +.+-+|.+.+++.|+|..|+..+|.+.+.. +.|+|++.+.
T Consensus       416 tlHlsnip~svsee~lk~~f~~~g~~vkafkff~----kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  416 TLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ----KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             heeeccCCcccchhHHHHhhhcCCceEEeeeecC----CCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            9999999999999999999998876544433322    224499999999999999999999988876 5899988764

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.73  E-value=1.1e-07  Score=80.34  Aligned_cols=86  Identities=17%  Similarity=0.331  Sum_probs=68.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEe-ecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC---CeEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM-RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA---GAQV  128 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~-~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~---gr~l  128 (314)
                      ....+||||.+||.++...||..+|..|---+...|. .++...-.+-+|||+|.+..+|++|+++||++.|+   ...|
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            3457999999999999999999999998544444443 23333334579999999999999999999999986   4778


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      .|++|+....
T Consensus       111 hiElAKSNtK  120 (284)
T KOG1457|consen  111 HIELAKSNTK  120 (284)
T ss_pred             EeeehhcCcc
Confidence            9988876544

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

Probab=98.71  E-value=1.1e-07  Score=71.49  Aligned_cols=79  Identities=15%  Similarity=0.240  Sum_probs=67.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhcc--CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC----CeEEEE
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQF--GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA----GAQVEV  130 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~--G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~----gr~l~V  130 (314)
                      +||.|.|||...|.++|.+++.+.  +...-+-|+.|..+..+.|||||.|.++++|.+..+.+++..+.    .+.++|
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            689999999999999999998654  66777889999889999999999999999999999998887764    355677


Q ss_pred             eecCC
Q 021295          131 KKAEP  135 (314)
Q Consensus       131 ~~a~~  135 (314)
                      .+|.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77654

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

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.68  E-value=1.7e-08  Score=86.25  Aligned_cols=72  Identities=26%  Similarity=0.631  Sum_probs=66.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      .+|||++||+.+.+.+|++||.+|++|.+|.|..        +|+||+|+++.+|+.||..||..+|.+-.|.|+++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            4799999999999999999999999999998863        48999999999999999999999999988999888854

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.68  E-value=2.4e-07  Score=87.18  Aligned_cols=124  Identities=23%  Similarity=0.398  Sum_probs=89.0

Q ss_pred             Cccc---EEEEEECCHHHHHHHHHccC-------------ccCCcEEEEeecCCC-----CCCCCCCCCcceEEEcCCCC
Q 021295            8 QPRG---FGFVTYADPSVVDKVIEDTH-------------IINGKQVEIKRTIPK-----GAVGSKDFKTKKIFVGGIPS   66 (314)
Q Consensus         8 ~~kG---~aFV~f~~~~~a~~A~~~~~-------------~i~g~~i~v~~~~~~-----~~~~~~~~~~~~l~V~nLp~   66 (314)
                      -+||   |+|+.|+++..+++.|..=.             .+..+.|.|......     ......-.+.+||||+.||.
T Consensus       301 ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvpr  380 (520)
T KOG0129|consen  301 PPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPR  380 (520)
T ss_pred             CCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCC
Confidence            3566   99999999999888776211             122222222221111     11112345778999999999


Q ss_pred             CCCHHHHHHHHh-ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHh----cCCeeeCCeEEEEee
Q 021295           67 SVNEDEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK----GNKLELAGAQVEVKK  132 (314)
Q Consensus        67 ~~~e~~l~~~F~-~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~----l~~~~~~gr~l~V~~  132 (314)
                      -++.+||..+|+ .||-|+-|-|=.|++-.-+||-+-|+|++..+-.+||++    |+..+|. ++|+|+.
T Consensus       381 pl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~-KRVEIkP  450 (520)
T KOG0129|consen  381 PLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDID-KRVEIKP  450 (520)
T ss_pred             cchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccc-eeeeecc
Confidence            999999999998 789999999999988888999999999999999999985    3333333 3566654

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.68  E-value=1.4e-08  Score=95.93  Aligned_cols=76  Identities=25%  Similarity=0.455  Sum_probs=67.9

Q ss_pred             CCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           49 VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        49 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ...++.+..+|+|-|||.++++++|+.+|+.||+|++|+.-+.     .++.+||+|-|..+|++|+++|+..+|.++.|
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            3345677899999999999999999999999999999765444     57899999999999999999999999999888


Q ss_pred             E
Q 021295          129 E  129 (314)
Q Consensus       129 ~  129 (314)
                      +
T Consensus       143 k  143 (549)
T KOG4660|consen  143 K  143 (549)
T ss_pred             c
Confidence            8

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=98.67  E-value=3.3e-08  Score=90.71  Aligned_cols=95  Identities=13%  Similarity=0.243  Sum_probs=75.9

Q ss_pred             EEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeec---CCCCC----------cceEEEEE
Q 021295           38 VEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRD---HSTSR----------SRGFGFIT  104 (314)
Q Consensus        38 i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~---~~~g~----------~rG~afV~  104 (314)
                      -+|++..|.+....++.+.++|.+-|||.+-.-|.|.++|..+|.|+.|+|+..   ..+.+          .+=+|+||
T Consensus       213 kKVrRisPlp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvE  292 (484)
T KOG1855|consen  213 KKVRRISPLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVE  292 (484)
T ss_pred             ceeeecCCCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhh
Confidence            345566666667777889999999999999999999999999999999999976   33221          24579999


Q ss_pred             eCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295          105 FDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus       105 F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      |++.++|.+|.+.|+....+-.-|+|+.
T Consensus       293 ye~~~~A~KA~e~~~~e~~wr~glkvkL  320 (484)
T KOG1855|consen  293 YEEVEAARKARELLNPEQNWRMGLKVKL  320 (484)
T ss_pred             hhhhHHHHHHHHhhchhhhhhhcchhhh
Confidence            9999999999999877665555555543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.64  E-value=4.5e-08  Score=87.62  Aligned_cols=80  Identities=11%  Similarity=0.278  Sum_probs=70.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G--~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ...++||+||-|++|++||.+.+...|  +|.+++++.++.++++||||+|...+..++++.++.|...+|.++.-.|..
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            345899999999999999999998776  577899999999999999999999999999999999999999997766654


Q ss_pred             cC
Q 021295          133 AE  134 (314)
Q Consensus       133 a~  134 (314)
                      ..
T Consensus       159 ~N  160 (498)
T KOG4849|consen  159 YN  160 (498)
T ss_pred             cc
Confidence            43

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.57  E-value=7.8e-08  Score=87.10  Aligned_cols=126  Identities=16%  Similarity=0.282  Sum_probs=93.6

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC--------C----CCCCcceEEEcCCCCCCCHH
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG--------S----KDFKTKKIFVGGIPSSVNED   71 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~--------~----~~~~~~~l~V~nLp~~~~e~   71 (314)
                      ..++-.+.+.|.|.|+|.-+-|++ ..+.+..+.|+|-.+...+-..        .    ....--.|.+.+||+++++.
T Consensus        97 ~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~  176 (508)
T KOG1365|consen   97 AQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATAL  176 (508)
T ss_pred             hhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchH
Confidence            456788999999999999999998 5567788888886554432111        1    11223467789999999999


Q ss_pred             HHHHHHhccC----CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           72 EFKDFFMQFG----DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        72 ~l~~~F~~~G----~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      |+.+||..--    .++.|-+++ +.+++..|-|||.|..+++|+.||.+ |...|.-|.|++..
T Consensus       177 dVv~FF~~~cpv~~g~egvLFV~-rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  177 DVVEFFGPPCPVTGGTEGVLFVT-RPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             HHHHhcCCCCcccCCccceEEEE-CCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            9999996432    334454444 35788999999999999999999998 77777777776643

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

Probab=98.57  E-value=3.3e-07  Score=81.08  Aligned_cols=113  Identities=22%  Similarity=0.484  Sum_probs=81.9

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC----CCCCCC----------------CCCCCcceE
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI----PKGAVG----------------SKDFKTKKI   59 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~----~~~~~~----------------~~~~~~~~l   59 (314)
                      +|+.|+++++||||+|.++++|..|++  +...+.++.|.|.+..    ++....                ........+
T Consensus       149 ~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (306)
T COG0724         149 RDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNL  228 (306)
T ss_pred             eccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhcccccccccccccccee
Confidence            567899999999999999999999999  3358899999999854    222211                123456789


Q ss_pred             EEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHH
Q 021295           60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL  114 (314)
Q Consensus        60 ~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a  114 (314)
                      ++.+++..++++++..+|..++.+..+.+...........+.++.++....+..+
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  283 (306)
T COG0724         229 YVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALES  283 (306)
T ss_pred             eccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhh
Confidence            9999999999999999999999997777766544333333333333333333333

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.49  E-value=2.5e-07  Score=89.74  Aligned_cols=85  Identities=21%  Similarity=0.364  Sum_probs=75.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCC---CCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS---TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~---~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ++.++.|||.||+..++|++|...|-.||+|..|+|+..+.   ..+.+-|+||.|.+..++++|++.|+++.+....|+
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            56788999999999999999999999999999999996543   345677999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      +-|.+...
T Consensus       251 ~gWgk~V~  258 (877)
T KOG0151|consen  251 LGWGKAVP  258 (877)
T ss_pred             eccccccc
Confidence            99986543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.47  E-value=1.9e-06  Score=78.96  Aligned_cols=81  Identities=20%  Similarity=0.308  Sum_probs=71.3

Q ss_pred             cceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           56 TKKIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        56 ~~~l~V~nLp~~-~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +..|.|.||..+ +|++.|..+|.-||+|.+|+|+.++.+     -|.|.+.+...|+-|++.|++..|.+++|+|.+.+
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd-----~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKD-----NALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCc-----ceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            467888998875 799999999999999999999988643     79999999999999999999999999999999887


Q ss_pred             CCCCCCC
Q 021295          135 PKKPNLP  141 (314)
Q Consensus       135 ~~~~~~~  141 (314)
                      -.....+
T Consensus       372 H~~vqlp  378 (492)
T KOG1190|consen  372 HTNVQLP  378 (492)
T ss_pred             CccccCC
Confidence            6655443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.47  E-value=6.5e-08  Score=95.51  Aligned_cols=111  Identities=15%  Similarity=0.269  Sum_probs=93.6

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD   82 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~   82 (314)
                      +.+++.||+|+|+|.+++++.+||. +...+.                    ...+|+|.|+|+..|.++|+.++.+++.
T Consensus       703 ~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~--------------------gK~~v~i~g~pf~gt~e~~k~l~~~~gn  762 (881)
T KOG0128|consen  703 KNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF--------------------GKISVAISGPPFQGTKEELKSLASKTGN  762 (881)
T ss_pred             hhccccccceeeEeecCCchhhhhhhhhhhhh--------------------hhhhhheeCCCCCCchHHHHhhccccCC
Confidence            4578999999999999999999998 211111                    1357899999999999999999999999


Q ss_pred             eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           83 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        83 v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      +++++++.. ..+++++.|+|.|.++.++.+++..++...+..+.+.|....+
T Consensus       763 ~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  763 VTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             ccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            999997776 4789999999999999999999998888778777777766444

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

Probab=98.47  E-value=3e-07  Score=74.86  Aligned_cols=47  Identities=32%  Similarity=0.674  Sum_probs=41.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ++|+.|+++|+||||+|+++++|++||+  +.++|+++.|+|+++.++.
T Consensus        67 ~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~  115 (144)
T PLN03134         67 IVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRP  115 (144)
T ss_pred             EecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCC
Confidence            4688999999999999999999999998  4568999999999887553

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.39  E-value=4.5e-07  Score=87.76  Aligned_cols=124  Identities=14%  Similarity=0.056  Sum_probs=93.2

Q ss_pred             ccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCC-----------------------------------CCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGA-----------------------------------VGSKD   53 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~-----------------------------------~~~~~   53 (314)
                      .|-++|+|...+++++|++ +...+..+.+++.......+                                   .....
T Consensus       352 tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~  431 (944)
T KOG4307|consen  352 TGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPG  431 (944)
T ss_pred             CCceEEEecCcchHHHHHhcCchhhhhcceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCC
Confidence            7889999999999999999 44444556665533211110                                   00122


Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~-v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ....+|||..||..+++.++.++|.+.-.|++ |.|.+. .+.+.+..|||+|..++++.+|+..-+++-+..+.|+|..
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            34569999999999999999999999888887 555544 5778889999999999888888877688888888888865


Q ss_pred             cC
Q 021295          133 AE  134 (314)
Q Consensus       133 a~  134 (314)
                      ..
T Consensus       511 i~  512 (944)
T KOG4307|consen  511 IA  512 (944)
T ss_pred             hh
Confidence            43

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.34  E-value=3.1e-07  Score=78.42  Aligned_cols=44  Identities=30%  Similarity=0.703  Sum_probs=39.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccC-ccCCcEEEEeecC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH-IINGKQVEIKRTI   44 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~-~i~g~~i~v~~~~   44 (314)
                      |+||+|++||||+||+|+|.++|++|+++.+ .|++++..++.+.
T Consensus        45 itd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   45 ITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLAS   89 (247)
T ss_pred             EeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhh
Confidence            6899999999999999999999999999665 7899999888764

>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=98.33  E-value=1.9e-06  Score=62.01  Aligned_cols=70  Identities=13%  Similarity=0.274  Sum_probs=47.1

Q ss_pred             ceEEEcCCCCCCCHHHHH----HHHhcc-CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           57 KKIFVGGIPSSVNEDEFK----DFFMQF-GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~----~~F~~~-G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ..|+|.|||.+.+...|+    +++..+ |+|..|.          .+.|+|.|.+++.|+.|++.|++.++-+++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999999887765    555566 4676652          2479999999999999999999999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            87544

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

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.18  E-value=4e-05  Score=69.63  Aligned_cols=114  Identities=14%  Similarity=0.195  Sum_probs=85.4

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC---------------------------------CCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG---------------------------------SKDF   54 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~---------------------------------~~~~   54 (314)
                      .+-|.||+.|..+++.|++  +...+-+.+|.++.+.......                                 .-..
T Consensus       325 ~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~  404 (494)
T KOG1456|consen  325 PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQP  404 (494)
T ss_pred             cceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccC
Confidence            4679999999999999999  4445677888886543221000                                 0134


Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ++++|..-|.|..+|||.|.++|..... ..+|+|...+ +.++. -..+||++.++|.+||.+||...|.+
T Consensus       405 Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k-serSs-sGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  405 PSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK-SERSS-SGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             CcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc-ccccc-cceeeeehHHHHHHHHHHhccccccC
Confidence            6788999999999999999999976543 4567777654 32222 46899999999999999999988876

>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=98.09  E-value=4.6e-06  Score=64.06  Aligned_cols=68  Identities=26%  Similarity=0.496  Sum_probs=43.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC-----CeeeCCeEEEEe
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN-----KLELAGAQVEVK  131 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~-----~~~~~gr~l~V~  131 (314)
                      .|.|.+|+..++.++|+++|++|++|.-|++.+...      .|+|.|.++++|++|++++.     .+.|.+..+.++
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            578889999999999999999999999999986532      79999999999999998753     345556555554

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

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.99  E-value=1.8e-05  Score=77.02  Aligned_cols=75  Identities=12%  Similarity=0.254  Sum_probs=65.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~-v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      +.|-|.|+|++++-+||.+||..|-.+.. |.|.+ .+.+++.|-|.|.|++.++|.+|.+.|++..|..++|+|..
T Consensus       868 ~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  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRR-NDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEee-cCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            47899999999999999999999965543 44444 47899999999999999999999999999999999998864

>smart00361 RRM_1 RNA recognition motif

Probab=97.99  E-value=1.2e-05  Score=57.00  Aligned_cols=39  Identities=21%  Similarity=0.375  Sum_probs=31.7

Q ss_pred             CCCCC--CCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEE
Q 021295            2 KDRKT--GQPRGFGFVTYADPSVVDKVIED--THIINGKQVEI   40 (314)
Q Consensus         2 ~d~~t--g~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v   40 (314)
                      +|+.|  +++|||+||+|.+.++|++|++.  ...+.++.|.+
T Consensus        27 ~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       27 IDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             eCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            45666  99999999999999999999994  34667777654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.92  E-value=3e-05  Score=69.55  Aligned_cols=84  Identities=19%  Similarity=0.416  Sum_probs=64.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHH----H--HHHHhccCCeEEEEEeecCCC-CCcceE--EEEEeCChHHHHHHHHhcCCee
Q 021295           52 KDFKTKKIFVGGIPSSVNEDE----F--KDFFMQFGDVQEHQIMRDHST-SRSRGF--GFITFDTEQAVDDLLAKGNKLE  122 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~----l--~~~F~~~G~v~~v~i~~~~~~-g~~rG~--afV~F~~~~~a~~a~~~l~~~~  122 (314)
                      ...+..-|||-.||..+..|+    |  .++|.+||+|+.|.|-+...+ ......  .+|+|.+.|+|..||.++++..
T Consensus       110 RVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~  189 (480)
T COG5175         110 RVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL  189 (480)
T ss_pred             eeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc
Confidence            445667889999999887666    3  388999999999888754311 111122  4999999999999999999999


Q ss_pred             eCCeEEEEeecCC
Q 021295          123 LAGAQVEVKKAEP  135 (314)
Q Consensus       123 ~~gr~l~V~~a~~  135 (314)
                      ++++.|+..+-..
T Consensus       190 ~DGr~lkatYGTT  202 (480)
T COG5175         190 LDGRVLKATYGTT  202 (480)
T ss_pred             ccCceEeeecCch
Confidence            9999999876544

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

Probab=97.88  E-value=3.2e-05  Score=51.63  Aligned_cols=52  Identities=17%  Similarity=0.489  Sum_probs=41.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHH
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL  115 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~  115 (314)
                      +.|-|.+.+.+..++.| ++|+.||+|+++.+...      .-+.+|+|+++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~vl-~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVL-EHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHH-HHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            56788888877775544 58889999999988732      238999999999999985

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.86  E-value=1.2e-06  Score=80.45  Aligned_cols=120  Identities=23%  Similarity=0.405  Sum_probs=98.4

Q ss_pred             ccEEEEEECCHHHHHHHHHcc---CccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEE
Q 021295           10 RGFGFVTYADPSVVDKVIEDT---HIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEH   86 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~~~---~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v   86 (314)
                      .+||||.+.+..+|.+|++..   .++.+++++++.++++..      .+++|-|.|+|....|+.|..++..|+.|+.+
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq------rsrk~Qirnippql~wevld~Ll~qyg~ve~~  110 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENC  110 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHh
Confidence            589999999999999999833   378899999998887644      35668999999999999999999999999887


Q ss_pred             EEee-cCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295           87 QIMR-DHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        87 ~i~~-~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      .++. +.+|    -..-|++.+.+.++.||++|+...|....++|.+.......
T Consensus       111 eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq~~  160 (584)
T KOG2193|consen  111 EQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDEQNA  160 (584)
T ss_pred             hhhccchHH----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchhhhh
Confidence            7642 2222    23457888899999999999999999999999887665443

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.86  E-value=2e-05  Score=78.71  Aligned_cols=120  Identities=16%  Similarity=0.265  Sum_probs=92.1

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCe
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDV   83 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v   83 (314)
                      -++-.-|+||.|.+.+.+..|+..  ...|..-.+++....+      +...++.|||+.|..|+....|..+|..||.|
T Consensus       409 ~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpi  482 (975)
T KOG0112|consen  409 IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPI  482 (975)
T ss_pred             CCcccchhhhhhhccccCcccchhhcCCccccCccccccccc------ccccceeeccCCCCCCChHHHHHHHhhccCcc
Confidence            345566899999998887776652  2233333333333322      45567899999999999999999999999999


Q ss_pred             EEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeecCCCC
Q 021295           84 QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKAEPKK  137 (314)
Q Consensus        84 ~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a~~~~  137 (314)
                      ..|.+-..      .-||+|.+++...+++|++.|....|.+  +.|.|.+|.+..
T Consensus       483 r~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  483 RIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             eeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCC
Confidence            99887543      3399999999999999999998888875  778998887654

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=97.85  E-value=8.6e-06  Score=77.29  Aligned_cols=46  Identities=28%  Similarity=0.697  Sum_probs=40.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~   46 (314)
                      |.|+.|+++|||+|++|.++++++.|++++  .++.+++|+|.++...
T Consensus        51 v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   51 VYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            468999999999999999999999999954  4899999999876543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=97.81  E-value=2.5e-05  Score=65.66  Aligned_cols=44  Identities=20%  Similarity=0.470  Sum_probs=36.4

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~   45 (314)
                      |++.||.||+||||+|++++.|+.|.+.|  ..+-++.|.+....|
T Consensus        84 RnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   84 RNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             cccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            78899999999999999999999998844  466677777765544

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.81  E-value=8.6e-07  Score=87.80  Aligned_cols=119  Identities=13%  Similarity=0.162  Sum_probs=84.1

Q ss_pred             EEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCCCC------CCcceEEEcCCCCCCCHHHHHHHHhccCCeE
Q 021295           12 FGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKD------FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ   84 (314)
Q Consensus        12 ~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~------~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~   84 (314)
                      +.+++++....++.|.. ....+..+.+.+..+.+++......      ....++||.||+..+.++||.+.|..++.|+
T Consensus       616 ~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e  695 (881)
T KOG0128|consen  616 QQQKVQSKHGSAESATVPAGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIE  695 (881)
T ss_pred             hhhhhhccccchhhcccccccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhh
Confidence            55666666666666665 3334445555554444443222211      2335889999999999999999999999888


Q ss_pred             EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           85 EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        85 ~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .|.|.....+.+.+|+|+|+|.+++.+.+||+....+.+....|-|
T Consensus       696 ~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i  741 (881)
T KOG0128|consen  696 VVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAI  741 (881)
T ss_pred             hHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhhe
Confidence            7777766678889999999999999999999876665555433333

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=97.76  E-value=2e-05  Score=66.17  Aligned_cols=42  Identities=29%  Similarity=0.678  Sum_probs=37.0

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      +|+.|..++|||||.|.+..+|++||+  +..+|+++.|.|+.+
T Consensus        47 rdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   47 RDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             cccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            689999999999999999999999998  445888999888754

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=97.75  E-value=3.3e-05  Score=68.25  Aligned_cols=43  Identities=21%  Similarity=0.550  Sum_probs=38.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      |+|+.|++|||||||+|+++.+...|.+  +...|+++.|.|+..
T Consensus       134 V~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen  134 VRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             eeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            5799999999999999999999999999  445889999998764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.72  E-value=9.7e-05  Score=69.92  Aligned_cols=67  Identities=28%  Similarity=0.552  Sum_probs=50.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeec--CCCCCcce---EEEEEeCChHHHHHHHHhcC
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRD--HSTSRSRG---FGFITFDTEQAVDDLLAKGN  119 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~--~~~g~~rG---~afV~F~~~~~a~~a~~~l~  119 (314)
                      ..-+++|||+.||++++|++|.+.|..||.|+.-+-.+.  +.---++|   |+|+.|+++.++++.|.++.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            345679999999999999999999999998763222111  11123567   99999999999998888753

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.68  E-value=7.8e-05  Score=63.24  Aligned_cols=47  Identities=21%  Similarity=0.493  Sum_probs=41.1

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHccC--ccCCcEEEEeecCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~--~i~g~~i~v~~~~~~~~   48 (314)
                      .|.++.+.|+|+||+|+..|+|.+||.+++  ++-++.|+|..+.|...
T Consensus        44 lDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   44 LDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             cchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccc
Confidence            467899999999999999999999999554  88899999999887643

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=97.66  E-value=4.9e-05  Score=68.06  Aligned_cols=52  Identities=23%  Similarity=0.505  Sum_probs=42.2

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHccC--ccCCcEEEEeecCCCCCCCCCCCCcc
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPKGAVGSKDFKTK   57 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~~~--~i~g~~i~v~~~~~~~~~~~~~~~~~   57 (314)
                      .--||||+||+|++++||++|-+++|  .|.+++|+|..++++-..++++....
T Consensus       132 ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV~n~K~~v~p~  185 (376)
T KOG0125|consen  132 ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARVHNKKKKVLPY  185 (376)
T ss_pred             cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhhccCCcccCCC
Confidence            44689999999999999999999555  89999999999988755555444333

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.64  E-value=1.5e-05  Score=67.43  Aligned_cols=111  Identities=22%  Similarity=0.361  Sum_probs=82.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccC--ccCCcEEEEeecCCCCCCCCCCCCcceEEEcC----CCCCCCHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPKGAVGSKDFKTKKIFVGG----IPSSVNEDEFK   74 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~--~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~~e~~l~   74 (314)
                      |.+-.+.+.| ||||.|+++..+.-|++.++  .+.++.+.                 .+++.++    |...++++.+.
T Consensus        41 ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q-----------------~~~r~G~shapld~r~~~ei~~  102 (267)
T KOG4454|consen   41 IPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ-----------------RTLRCGNSHAPLDERVTEEILY  102 (267)
T ss_pred             CCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhh-----------------cccccCCCcchhhhhcchhhhe
Confidence            4455678888 99999999999999998433  33333333                 2344445    66778899999


Q ss_pred             HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           75 DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        75 ~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      +.|+..+.|+.+++.++.+ ++++-+.||++...-++-.++.....+.+--+++.+
T Consensus       103 ~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~  157 (267)
T KOG4454|consen  103 EVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTI  157 (267)
T ss_pred             eeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhhhcccCcCCCCccc
Confidence            9999999999999998854 788889999988777777777776665554444444

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.59  E-value=0.00015  Score=62.96  Aligned_cols=93  Identities=14%  Similarity=0.293  Sum_probs=73.1

Q ss_pred             ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCCh
Q 021295           29 DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE  108 (314)
Q Consensus        29 ~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~  108 (314)
                      +.....++.+.|..+..           ..|+|.||+.-++.|.|.+.|+.|++|+...++.| ...++.+-.+|+|...
T Consensus        15 d~~~~~~~~lr~rfa~~-----------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k   82 (275)
T KOG0115|consen   15 DGRFPKGRSLRVRFAMH-----------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKK   82 (275)
T ss_pred             CCCCCCCCceEEEeecc-----------ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcc
Confidence            55567888888887652           57999999999999999999999999998777777 4567788899999999


Q ss_pred             HHHHHHHHhcCC----eeeCCeEEEEeec
Q 021295          109 QAVDDLLAKGNK----LELAGAQVEVKKA  133 (314)
Q Consensus       109 ~~a~~a~~~l~~----~~~~gr~l~V~~a  133 (314)
                      -.+.+|+..++.    .++..+++-|..+
T Consensus        83 ~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   83 PNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             hhHHHHHHHhccCccccCCCCCccCCChh
Confidence            999999987633    2234455544433

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.57  E-value=2e-05  Score=64.97  Aligned_cols=46  Identities=24%  Similarity=0.553  Sum_probs=40.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccC--ccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~--~i~g~~i~v~~~~~~   46 (314)
                      |+|+.||+||||||+.|+|..+...|+.+++  .|.+++|+|++....
T Consensus        68 iRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Y  115 (219)
T KOG0126|consen   68 IRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNY  115 (219)
T ss_pred             EecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccc
Confidence            7899999999999999999999999998554  788999999875544

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.57  E-value=0.00037  Score=66.62  Aligned_cols=82  Identities=13%  Similarity=0.178  Sum_probs=65.5

Q ss_pred             CCCcceEEEcCCCCCC--CH----HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC-C
Q 021295           53 DFKTKKIFVGGIPSSV--NE----DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-G  125 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~--~e----~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~-g  125 (314)
                      +.-...|+|.++|.--  ..    ..|.++|+++|+|+.+.++.+.+++ .+||.|++|.+..+|+.|++.||+..|+ .
T Consensus        55 eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   55 EGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             CCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            3456789999999743  22    3456889999999999999886555 9999999999999999999999998876 5


Q ss_pred             eEEEEeecCC
Q 021295          126 AQVEVKKAEP  135 (314)
Q Consensus       126 r~l~V~~a~~  135 (314)
                      +.+.|..-++
T Consensus       134 Htf~v~~f~d  143 (698)
T KOG2314|consen  134 HTFFVRLFKD  143 (698)
T ss_pred             ceEEeehhhh
Confidence            7777764433

>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=97.52  E-value=0.00045  Score=52.34  Aligned_cols=78  Identities=26%  Similarity=0.408  Sum_probs=52.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEE-EeecC------CCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe-
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQ-IMRDH------STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA-  126 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~-i~~~~------~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr-  126 (314)
                      ....|.|=+.|.+ ....|.++|++||+|.+.. +.++.      ..........|+|+++.+|++||.+ |+..|.+. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            4566888889888 5578889999999998774 11100      0011234889999999999999999 99999885 


Q ss_pred             EEEEeecC
Q 021295          127 QVEVKKAE  134 (314)
Q Consensus       127 ~l~V~~a~  134 (314)
                      .|.|.+++
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            45677764

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.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.52  E-value=3.7e-05  Score=66.75  Aligned_cols=64  Identities=13%  Similarity=0.250  Sum_probs=52.3

Q ss_pred             HHHHHHHh-ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           71 DEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        71 ~~l~~~F~-~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      |||..+|+ +|++|+++.|..+. ....+|-++|.|..+++|++|++.||+-++.+++|...+..-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            34444454 89999999888764 345688999999999999999999999999999998876543

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=97.43  E-value=0.00016  Score=56.88  Aligned_cols=47  Identities=26%  Similarity=0.461  Sum_probs=40.8

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~   48 (314)
                      .|+.|+-.||||+|+|++.++|++|+..+  .++.++.|.|+|+..+.+
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            47789999999999999999999999944  488999999999876544

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=97.40  E-value=0.00021  Score=55.66  Aligned_cols=43  Identities=21%  Similarity=0.386  Sum_probs=37.8

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      .|+.|..+.|||||+|-+.++|+.||+  +.+.++.+.|.++|..
T Consensus        70 Ldr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   70 LDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             cccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            488899999999999999999999999  6667888888887754

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.37  E-value=0.0012  Score=45.29  Aligned_cols=57  Identities=14%  Similarity=0.330  Sum_probs=46.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhcc---CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQF---GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG  118 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~---G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l  118 (314)
                      ....+|+|.+|. +++.+||+.+|..|   .....|..+.|.       -|-|.|.++++|.+||.+|
T Consensus         3 ~rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    3 IRPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            446789999984 58889999999988   235578888774       5999999999999999875

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.37  E-value=0.00032  Score=64.29  Aligned_cols=79  Identities=16%  Similarity=0.199  Sum_probs=60.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC---CCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST---SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~---g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ...|-|.||..+++.++|+.+|.-.|+|.++.|+.+..+   ....-.|||.|.+..++..|..+-|.+.|+-..|++.+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            347899999999999999999999999999999875332   22345899999999999888776555555544455544


Q ss_pred             cC
Q 021295          133 AE  134 (314)
Q Consensus       133 a~  134 (314)
                      ..
T Consensus        87 ~~   88 (479)
T KOG4676|consen   87 GD   88 (479)
T ss_pred             CC
Confidence            43

>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=97.37  E-value=0.00028  Score=51.97  Aligned_cols=66  Identities=18%  Similarity=0.384  Sum_probs=47.1

Q ss_pred             EEEEECCHHHHHHHHH-ccC--ccCCcEEEEeecCCCCCC-----CCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295           13 GFVTYADPSVVDKVIE-DTH--IINGKQVEIKRTIPKGAV-----GSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus        13 aFV~f~~~~~a~~A~~-~~~--~i~g~~i~v~~~~~~~~~-----~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+|+|.++..|++.++ ..+  .++..++.|+.+.-....     -......++|.|.+||..++|++|+|.++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            7899999999999998 333  455666665543221111     11456788999999999999999988643

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=97.37  E-value=0.00016  Score=59.44  Aligned_cols=40  Identities=25%  Similarity=0.582  Sum_probs=34.7

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      .+.|||||||+++.+|++|+.  +..+|.+..|.|+++.-..
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            688999999999999999998  5568999999999876543

>smart00360 RRM RNA recognition motif

Probab=97.37  E-value=0.00038  Score=47.80  Aligned_cols=38  Identities=26%  Similarity=0.679  Sum_probs=30.4

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEE
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEI   40 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v   40 (314)
                      ++.+++++++|||+|.+.++|++|++.+  ..+.++.|.|
T Consensus        31 ~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360       31 DKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            4457899999999999999999999843  4566666654

>PF13893 RRM_5: RNA recognition motif

Probab=97.32  E-value=0.00049  Score=46.18  Aligned_cols=34  Identities=32%  Similarity=0.620  Sum_probs=30.3

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      +++|||+|.+.++|++|++  +...+.+++|.|+++
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            6999999999999999998  556889999998864

(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 ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=97.30  E-value=0.0003  Score=49.36  Aligned_cols=37  Identities=30%  Similarity=0.654  Sum_probs=29.8

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEE
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVE   39 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~   39 (314)
                      +++. ++++++|||+|+++++|++|++..  ..+.++.|+
T Consensus        32 ~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   32 KNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             ESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             eeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            3444 899999999999999999999933  467777663

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 ....

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.27  E-value=0.00011  Score=63.78  Aligned_cols=73  Identities=15%  Similarity=0.366  Sum_probs=61.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC--------CCcceE----EEEEeCChHHHHHHHHhcCCee
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST--------SRSRGF----GFITFDTEQAVDDLLAKGNKLE  122 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~--------g~~rG~----afV~F~~~~~a~~a~~~l~~~~  122 (314)
                      .+-.|||++||+.++...|+++|+.||+|-+|.|.+...+        +..+..    +.|||.+...|+.+.+.||+..
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            4568999999999999999999999999999998876544        222222    4699999999999999999999


Q ss_pred             eCCeE
Q 021295          123 LAGAQ  127 (314)
Q Consensus       123 ~~gr~  127 (314)
                      |.++.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98864

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.23  E-value=0.0016  Score=52.45  Aligned_cols=74  Identities=20%  Similarity=0.342  Sum_probs=51.7

Q ss_pred             CCcceEEEcCCCC------CCCH---HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC
Q 021295           54 FKTKKIFVGGIPS------SVNE---DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA  124 (314)
Q Consensus        54 ~~~~~l~V~nLp~------~~~e---~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~  124 (314)
                      ++.-||.|.-+.+      ...+   ++|.+.|+.||+|.-|+++.+        .-.|+|.+-++|.+|+++ +++.++
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~-dg~~v~   95 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSL-DGIQVN   95 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHG-CCSEET
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHcc-CCcEEC
Confidence            3445666655541      2222   366788889999998888765        479999999999999998 899999


Q ss_pred             CeEEEEeecCCC
Q 021295          125 GAQVEVKKAEPK  136 (314)
Q Consensus       125 gr~l~V~~a~~~  136 (314)
                      ++.|+|+...+.
T Consensus        96 g~~l~i~LKtpd  107 (146)
T PF08952_consen   96 GRTLKIRLKTPD  107 (146)
T ss_dssp             TEEEEEEE----
T ss_pred             CEEEEEEeCCcc
Confidence            999999876553

; PDB: 1UFW_A 2DNR_A.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.21  E-value=0.0011  Score=58.69  Aligned_cols=65  Identities=20%  Similarity=0.162  Sum_probs=53.4

Q ss_pred             HHHHHHHHhccCCeEEEEEeecCCCCCcc-eEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           70 EDEFKDFFMQFGDVQEHQIMRDHSTSRSR-GFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        70 e~~l~~~F~~~G~v~~v~i~~~~~~g~~r-G~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      |+++++.+++||+|..|.|..++.....+ .-.||+|+..++|.+|+-.||+..|.++.+...+-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            46788999999999999888775433222 347999999999999999999999999998876644

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=97.14  E-value=0.001  Score=63.63  Aligned_cols=71  Identities=14%  Similarity=0.220  Sum_probs=56.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhc--cCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc--CCeeeCCeEEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQ--FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQVE  129 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~--~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l--~~~~~~gr~l~  129 (314)
                      .+.+.|+|+.||..+.+|+|+.||+.  |-++++|.+..+.       -=||+|++.++|++|.+.|  ...+|.+++|+
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            34567888999999999999999964  6788888877653       2599999999999998876  33567777775


Q ss_pred             Ee
Q 021295          130 VK  131 (314)
Q Consensus       130 V~  131 (314)
                      ..
T Consensus       246 AR  247 (684)
T KOG2591|consen  246 AR  247 (684)
T ss_pred             hh
Confidence            54

>PLN03213 repressor of silencing 3; Provisional

Probab=97.12  E-value=0.00024  Score=66.94  Aligned_cols=41  Identities=15%  Similarity=0.509  Sum_probs=34.2

Q ss_pred             CCCCCcccEEEEEECCH--HHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            4 RKTGQPRGFGFVTYADP--SVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~--~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +.|+  ||||||+|.+.  +++++||+  +..++.++.|+|..+.++
T Consensus        44 RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213         44 RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            4577  99999999987  68899998  556889999999887654

>PF00076 RRM_1: RNA recognition motif

Probab=97.08  E-value=0.00083  Score=46.66  Aligned_cols=34  Identities=26%  Similarity=0.701  Sum_probs=28.6

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEE
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQV   38 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i   38 (314)
                      .++++++||||+|++.++|++|++  +...+.++.|
T Consensus        34 ~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~i   69 (70)
T PF00076_consen   34 SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKI   69 (70)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCc
Confidence            578999999999999999999999  4446666665

(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 ....

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=97.00  E-value=0.021  Score=58.26  Aligned_cols=14  Identities=29%  Similarity=0.539  Sum_probs=6.6

Q ss_pred             CCCcccEEEEEECC
Q 021295            6 TGQPRGFGFVTYAD   19 (314)
Q Consensus         6 tg~~kG~aFV~f~~   19 (314)
                      .++.++|+.-.|++
T Consensus       898 ~g~q~~~~g~kfsd  911 (1282)
T KOG0921|consen  898 SGTQRKFAGNKFSD  911 (1282)
T ss_pred             ccchhhcccccccc
Confidence            34444555444444

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.00  E-value=0.00067  Score=65.31  Aligned_cols=79  Identities=6%  Similarity=0.156  Sum_probs=63.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHh-ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee---CCe
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL---AGA  126 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~-~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~---~gr  126 (314)
                      +....++.|+|.||-.-+|.-+|+.++. ..+.|++.+|-+      -|-.|||.|.+.++|.+.+.+||++.+   +.+
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK  512 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPK  512 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCc
Confidence            3556778999999999999999999998 566777775432      244799999999999999999999876   457


Q ss_pred             EEEEeecCC
Q 021295          127 QVEVKKAEP  135 (314)
Q Consensus       127 ~l~V~~a~~  135 (314)
                      .|+|.++..
T Consensus       513 ~L~adf~~~  521 (718)
T KOG2416|consen  513 HLIADFVRA  521 (718)
T ss_pred             eeEeeecch
Confidence            788877654

>PLN03120 nucleic acid binding protein; Provisional

Probab=96.88  E-value=0.0037  Score=55.28  Aligned_cols=40  Identities=18%  Similarity=0.262  Sum_probs=34.5

Q ss_pred             CcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~   47 (314)
                      .+++||||+|+++++|+.||. +...|.++.|.|.++....
T Consensus        41 ~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120         41 ERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCCC
Confidence            367999999999999999998 6678999999999876443

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

Probab=96.85  E-value=0.0038  Score=45.13  Aligned_cols=57  Identities=18%  Similarity=0.338  Sum_probs=41.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK  120 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~  120 (314)
                      ...||---+|.++...||.++|+.||.|.--.| .|  |     -|||.+.+.+.|..|+..++.
T Consensus         8 RdHVFhltFPkeWK~~DI~qlFspfG~I~VsWi-~d--T-----SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLTFPKEWKTSDIYQLFSPFGQIYVSWI-ND--T-----SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE--TT--HHHHHHHCCCCCCEEEEEE-CT--T-----EEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEeCchHhhhhhHHHHhccCCcEEEEEE-cC--C-----cEEEEeecHHHHHHHHHHhcc
Confidence            344555559999999999999999999875444 33  2     799999999999999887654

; 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.

>smart00362 RRM_2 RNA recognition motif

Probab=96.77  E-value=0.0027  Score=43.54  Aligned_cols=34  Identities=26%  Similarity=0.643  Sum_probs=27.4

Q ss_pred             CCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEE
Q 021295            7 GQPRGFGFVTYADPSVVDKVIED--THIINGKQVEI   40 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v   40 (314)
                      +.++++|||+|.+.++|++|++.  ...+.++.|.|
T Consensus        36 ~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362       36 GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            67889999999999999999983  34566666654

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=96.72  E-value=0.00064  Score=59.04  Aligned_cols=43  Identities=21%  Similarity=0.762  Sum_probs=35.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~   43 (314)
                      |+|+.|+++|||.||.|.+++++..||+++  ..+..+.|.++.+
T Consensus       223 iRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  223 IRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            689999999999999999999999999954  3556666655543

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=96.54  E-value=0.023  Score=51.58  Aligned_cols=6  Identities=17%  Similarity=0.075  Sum_probs=2.4

Q ss_pred             CHHHHH
Q 021295           69 NEDEFK   74 (314)
Q Consensus        69 ~e~~l~   74 (314)
                      +|++|+
T Consensus       199 ~w~~iE  204 (465)
T KOG3973|consen  199 TWPEIE  204 (465)
T ss_pred             hHHHHH
Confidence            344443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.42  E-value=0.00085  Score=60.67  Aligned_cols=84  Identities=18%  Similarity=0.351  Sum_probs=63.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH---HHHhccCCeEEEEEeecCCCCC---cceEEEEEeCChHHHHHHHHhcCCeeeCCe
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFK---DFFMQFGDVQEHQIMRDHSTSR---SRGFGFITFDTEQAVDDLLAKGNKLELAGA  126 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~---~~F~~~G~v~~v~i~~~~~~g~---~rG~afV~F~~~~~a~~a~~~l~~~~~~gr  126 (314)
                      .++.+.+||-.|+..+..+++.   +.|.+|+.|..|.+..+..+..   ..--++|+|+..|+|..||...+++.++++
T Consensus        74 vVqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   74 VVQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhh
Confidence            3556778999999886555543   6688899999999988762111   112379999999999999999999999998


Q ss_pred             EEEEeecCCC
Q 021295          127 QVEVKKAEPK  136 (314)
Q Consensus       127 ~l~V~~a~~~  136 (314)
                      .|++.+...+
T Consensus       154 ~lka~~gttk  163 (327)
T KOG2068|consen  154 ALKASLGTTK  163 (327)
T ss_pred             hhHHhhCCCc
Confidence            8777665554

>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=96.37  E-value=0.008  Score=41.36  Aligned_cols=34  Identities=24%  Similarity=0.620  Sum_probs=27.6

Q ss_pred             CcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEe
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIK   41 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~   41 (314)
                      .++++|||+|.+.++|+.|++..  ..++++.+.|.
T Consensus        38 ~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590          38 KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            67999999999999999999843  34677777664

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).

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.37  E-value=0.0092  Score=50.21  Aligned_cols=83  Identities=14%  Similarity=0.177  Sum_probs=50.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhc-cCCe---EEEEEeecCCC--CCcceEEEEEeCChHHHHHHHHhcCCeeeCC---
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQ-FGDV---QEHQIMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKLELAG---  125 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~-~G~v---~~v~i~~~~~~--g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g---  125 (314)
                      ...+|.|++||+.+||+++.+.++. +...   ..+.-.....+  ...---|+|.|.+.+++...++.++++.|.+   
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            4568999999999999999997765 4443   23331122111  1123459999999999999999999977644   


Q ss_pred             --eEEEEeecCCCC
Q 021295          126 --AQVEVKKAEPKK  137 (314)
Q Consensus       126 --r~l~V~~a~~~~  137 (314)
                        ....|++|.-++
T Consensus        86 ~~~~~~VE~Apyqk   99 (176)
T PF03467_consen   86 NEYPAVVEFAPYQK   99 (176)
T ss_dssp             -EEEEEEEE-SS--
T ss_pred             CCcceeEEEcchhc
Confidence              345666666543

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.31  E-value=0.021  Score=45.61  Aligned_cols=74  Identities=11%  Similarity=0.140  Sum_probs=54.9

Q ss_pred             CCCCcceEEEcCCCCCCC-HHH---HHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE
Q 021295           52 KDFKTKKIFVGGIPSSVN-EDE---FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ  127 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~-e~~---l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~  127 (314)
                      ++++..+|.|.=|..++. .+|   |...++.||+|+.|.++-.       --|+|+|++..+|-+|+.+++. ..-+..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            467788999987777653 244   4566789999999988743       2699999999999999998765 445555


Q ss_pred             EEEeec
Q 021295          128 VEVKKA  133 (314)
Q Consensus       128 l~V~~a  133 (314)
                      +.+.|.
T Consensus       154 ~qCsWq  159 (166)
T PF15023_consen  154 FQCSWQ  159 (166)
T ss_pred             EEeecc
Confidence            665553

>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=96.17  E-value=0.062  Score=41.47  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=52.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      .+..+.|..+|+.++-++|..+.+.+- .|+.++|++|...  .+=.+.|+|.+.++|++-.+..|+..++.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p--nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP--NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC--ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344555666677777788877777664 4678899887432  45578999999999999999999977655

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.16  E-value=0.0015  Score=65.71  Aligned_cols=80  Identities=16%  Similarity=0.264  Sum_probs=62.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ....+++||++||+..+++.+|+..|.++|.|++|+|-+.+.. +---|+||.|.+.+.+-+|+..+....|..-.+++.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~-~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIK-TESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCC-cccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            3456789999999999999999999999999999999776432 233489999999988888877776666654444443


Q ss_pred             e
Q 021295          132 K  132 (314)
Q Consensus       132 ~  132 (314)
                      +
T Consensus       447 l  447 (975)
T KOG0112|consen  447 L  447 (975)
T ss_pred             c
Confidence            3

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=95.93  E-value=0.028  Score=40.10  Aligned_cols=59  Identities=17%  Similarity=0.332  Sum_probs=36.8

Q ss_pred             CCCCHHHHHHHHhccCC-----eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           66 SSVNEDEFKDFFMQFGD-----VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        66 ~~~~e~~l~~~F~~~G~-----v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ..++..+|..++.+...     |-.|+|..+        |+||+-... .++++++.|++..+.+++|+|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            35788899988877643     557888765        899988654 788899999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.89  E-value=0.00041  Score=63.57  Aligned_cols=64  Identities=14%  Similarity=0.056  Sum_probs=50.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ++|+|.+|+..+...++.+.|..+|+|...++....    ..-+|-|+|........|+.. ++.++.-
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~----~s~~c~~sf~~qts~~halr~-~gre~k~  215 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTASKS----RSSSCSHSFRKQTSSKHALRS-HGRERKR  215 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccC----CCcchhhhHhhhhhHHHHHHh-cchhhhh
Confidence            789999999999999999999999999877665332    223677999988888888877 4545443

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.55  E-value=0.0099  Score=54.11  Aligned_cols=45  Identities=18%  Similarity=0.494  Sum_probs=39.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      |+|++|+.+--||||+|++.++.++|.-  +...|+.++|.|..+.+
T Consensus       272 IRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  272 IRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             EecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            6899999999999999999999999986  44578999999987654

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.45  E-value=0.0098  Score=58.28  Aligned_cols=80  Identities=19%  Similarity=0.193  Sum_probs=66.9

Q ss_pred             CCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           44 IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        44 ~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      +|.........+..+|||+||...+.++-++.++.++|.|..+..+.         |.|.+|+.+.....|+..|+...+
T Consensus        28 ~p~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~   98 (668)
T KOG2253|consen   28 VPIQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNI   98 (668)
T ss_pred             cCCcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCC
Confidence            33344444556778999999999999999999999999988766543         899999999999999999999999


Q ss_pred             CCeEEEEee
Q 021295          124 AGAQVEVKK  132 (314)
Q Consensus       124 ~gr~l~V~~  132 (314)
                      +++.|.+..
T Consensus        99 ~~~kl~~~~  107 (668)
T KOG2253|consen   99 DDQKLIENV  107 (668)
T ss_pred             Ccchhhccc
Confidence            888877655

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.37  E-value=0.0094  Score=56.22  Aligned_cols=74  Identities=16%  Similarity=0.276  Sum_probs=59.6

Q ss_pred             CcceEEEcCCCCCC-CHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           55 KTKKIFVGGIPSSV-NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        55 ~~~~l~V~nLp~~~-~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +.+.|-|..+|..+ +-++|..+|.+||+|+.|.|-...+      -|+|+|.+..+|-+|... +...|+++.|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~s-~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYAS-HGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhcc-ccceecCceeEEEEe
Confidence            44566666777765 5689999999999999988765422      599999999999777665 788999999999998


Q ss_pred             CC
Q 021295          134 EP  135 (314)
Q Consensus       134 ~~  135 (314)
                      .+
T Consensus       444 np  445 (526)
T KOG2135|consen  444 NP  445 (526)
T ss_pred             cC
Confidence            77

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.34  E-value=0.016  Score=53.96  Aligned_cols=75  Identities=20%  Similarity=0.406  Sum_probs=58.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC-eeeCCeEEEEeecC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-LELAGAQVEVKKAE  134 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~-~~~~gr~l~V~~a~  134 (314)
                      ++||++||.+.++..||+.+|...-. +..-.|+       ..+||||.+.+...+.+|++.++. +++.++.++|....
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            47999999999999999999975411 1111122       246999999999999999998866 56889999998877


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      +++.
T Consensus        75 ~kkq   78 (584)
T KOG2193|consen   75 PKKQ   78 (584)
T ss_pred             hHHH
Confidence            7654

>PLN03121 nucleic acid binding protein; Provisional

Probab=95.30  E-value=0.04  Score=48.14  Aligned_cols=39  Identities=21%  Similarity=0.247  Sum_probs=33.3

Q ss_pred             CCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      +++++||||+|+++++|+.|+. +..+|..+.|.|.....
T Consensus        41 ~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121         41 GEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            5667899999999999999998 66788999999887543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.20  E-value=0.12  Score=46.33  Aligned_cols=74  Identities=20%  Similarity=0.301  Sum_probs=52.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe-EEEEeecC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA-QVEVKKAE  134 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr-~l~V~~a~  134 (314)
                      ..=|.|-.+|.... ..|..+|++||+|+++....+      --+-+|.|.+..+|++||.+ |+..|++. -|-|+.+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~n------gNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSN------GNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCC------CceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            34455556665443 466789999999987765522      23889999999999999999 77777764 45666665


Q ss_pred             CCC
Q 021295          135 PKK  137 (314)
Q Consensus       135 ~~~  137 (314)
                      ++.
T Consensus       269 Dks  271 (350)
T KOG4285|consen  269 DKS  271 (350)
T ss_pred             CHH
Confidence            553

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.09  E-value=0.093  Score=44.40  Aligned_cols=63  Identities=11%  Similarity=0.171  Sum_probs=46.0

Q ss_pred             CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEEEEeecCCC
Q 021295           68 VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVEVKKAEPK  136 (314)
Q Consensus        68 ~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l~V~~a~~~  136 (314)
                      ...+.|+++|..+..+..+.+++.      -.-..|.|.+.++|.+|...|+  ...+.+..|+|-++...
T Consensus         7 ~~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    7 DNLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             --HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hhHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            345889999999999988877754      2258999999999999999999  89999999999877443

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.

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=95.03  E-value=0.028  Score=56.12  Aligned_cols=71  Identities=21%  Similarity=0.355  Sum_probs=50.1

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC-CCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS-KDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~-~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      -++++|||++...++|++||.  +.+.+..+.|++.|+..+....+ ++.-...|=|.-|||+.-.++|+.|++
T Consensus       455 ~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  455 PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcchhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            579999999999999999998  45688899999999987654431 111122333445688754455776665

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.73  E-value=0.023  Score=57.18  Aligned_cols=77  Identities=16%  Similarity=0.177  Sum_probs=64.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee--eCCeEEEEeecCC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE--LAGAQVEVKKAEP  135 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~--~~gr~l~V~~a~~  135 (314)
                      +..+.|++..++-..|..+|++|+.|+.++.+++-.      .|.|+|++.+.|-.|+++|++.+  +.+-+.+|.+|+.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            456667777778888999999999999999998843      79999999999999999998876  4678889988887


Q ss_pred             CCCCC
Q 021295          136 KKPNL  140 (314)
Q Consensus       136 ~~~~~  140 (314)
                      -+...
T Consensus       374 ~~~~e  378 (1007)
T KOG4574|consen  374 LPMYE  378 (1007)
T ss_pred             ccccc
Confidence            65443

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=94.44  E-value=0.58  Score=48.26  Aligned_cols=10  Identities=10%  Similarity=0.046  Sum_probs=4.1

Q ss_pred             EEEEeecCCC
Q 021295          127 QVEVKKAEPK  136 (314)
Q Consensus       127 ~l~V~~a~~~  136 (314)
                      .|++..|...
T Consensus      1135 dIs~pSAa~i 1144 (1282)
T KOG0921|consen 1135 DISRPSAADI 1144 (1282)
T ss_pred             Hhcccccccc
Confidence            3444444433

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.41  E-value=0.054  Score=49.36  Aligned_cols=36  Identities=33%  Similarity=0.600  Sum_probs=31.9

Q ss_pred             ccEEEEEECCHHHHHHHHH---ccCccCCcEEEEeecCC
Q 021295           10 RGFGFVTYADPSVVDKVIE---DTHIINGKQVEIKRTIP   45 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~---~~~~i~g~~i~v~~~~~   45 (314)
                      +++|||+|.+.++|++|.+   +...|++++|.|+|..+
T Consensus       264 ~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  264 KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            5699999999999999998   44488999999999887

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=94.35  E-value=0.041  Score=49.91  Aligned_cols=81  Identities=17%  Similarity=0.178  Sum_probs=66.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ...++|++++.+.+.+.++..++.+.+.+..+.+........+++++.|.|...+.+..||+......+..+.+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999999999999988888877777788899999999999999999999855545555555444433


Q ss_pred             C
Q 021295          135 P  135 (314)
Q Consensus       135 ~  135 (314)
                      .
T Consensus       167 ~  167 (285)
T KOG4210|consen  167 R  167 (285)
T ss_pred             c
Confidence            3

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.20  E-value=0.42  Score=45.22  Aligned_cols=69  Identities=16%  Similarity=0.328  Sum_probs=58.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhcc-CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQF-GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~-G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ....|+|--+|..++-.||..|...+ -.|.+|+|++|...  .+=.+.|+|.+.++|....+.+|+..|+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            37889999999999999999998765 46889999997543  34468999999999999999999987765

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=93.82  E-value=0.092  Score=50.69  Aligned_cols=81  Identities=12%  Similarity=0.148  Sum_probs=52.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhc-cCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee---eCC-eEEEE
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQ-FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE---LAG-AQVEV  130 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~-~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~---~~g-r~l~V  130 (314)
                      ..++.|.|+|...|...|.+..++ .+.=+-+.++.|-.+....|||||.|.+++++..+.++.|+..   |.. +.++|
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            344455555555444444433222 2333456677777777788999999999999999999988865   333 44566


Q ss_pred             eecCCC
Q 021295          131 KKAEPK  136 (314)
Q Consensus       131 ~~a~~~  136 (314)
                      .+|.-+
T Consensus       468 tYArIQ  473 (549)
T KOG4660|consen  468 TYARIQ  473 (549)
T ss_pred             ehhhhh
Confidence            666544

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.74  E-value=0.31  Score=45.30  Aligned_cols=59  Identities=8%  Similarity=0.170  Sum_probs=47.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHh
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK  117 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~  117 (314)
                      +..-...|=|-++|.....+||..+|+.|.. =.+|..+.|.       .||-.|++...|..||-.
T Consensus       387 e~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  387 ESDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             cccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            3334567888899999999999999999854 3456666553       799999999999999886

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=93.61  E-value=0.051  Score=49.71  Aligned_cols=45  Identities=27%  Similarity=0.514  Sum_probs=37.0

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +||+|.++|+-|.|+|+|+.+|++||+  +-..+.+..|+|..+..+
T Consensus       108 ~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  108 TDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERR  154 (351)
T ss_pred             ccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhc
Confidence            688999999999999999999999998  555677777766655444

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=93.56  E-value=0.04  Score=44.84  Aligned_cols=83  Identities=14%  Similarity=0.160  Sum_probs=61.7

Q ss_pred             cccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCCCCCCcce--EEEcCCCCC-CCHHHHHHHHhccCCeE
Q 021295            9 PRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKK--IFVGGIPSS-VNEDEFKDFFMQFGDVQ   84 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~--l~V~nLp~~-~~e~~l~~~F~~~G~v~   84 (314)
                      ..++..++|.++++++++++ ....+.+..+.++.-.+.............  |-|.+||.. .+++.|+++.+.+|++.
T Consensus        54 ~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i  133 (153)
T PF14111_consen   54 GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPI  133 (153)
T ss_pred             CCCeEEEEEEeccceeEEEecccccccccchhhhhhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeE
Confidence            46788899999999999998 555677777777766655444333333333  556899997 58888999999999999


Q ss_pred             EEEEeec
Q 021295           85 EHQIMRD   91 (314)
Q Consensus        85 ~v~i~~~   91 (314)
                      +++....
T Consensus       134 ~vD~~t~  140 (153)
T PF14111_consen  134 EVDENTL  140 (153)
T ss_pred             EEEcCCC
Confidence            9887644

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.40  E-value=0.26  Score=47.91  Aligned_cols=76  Identities=13%  Similarity=0.209  Sum_probs=58.8

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHHhcc----CCeEEEEEeecCC----------CCC---------------------
Q 021295           53 DFKTKKIFVGGIPSS-VNEDEFKDFFMQF----GDVQEHQIMRDHS----------TSR---------------------   96 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~-~~e~~l~~~F~~~----G~v~~v~i~~~~~----------~g~---------------------   96 (314)
                      ...+++|-|.||.|+ +..+||..+|..|    |.|..|.|++...          ++.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            346789999999997 7889999999887    5788888765411          111                     


Q ss_pred             ---------------c-ceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           97 ---------------S-RGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        97 ---------------~-rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                                     . -=||+|+|++.++|.++.+.++++++....+
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~  298 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSAN  298 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccc
Confidence                           0 1279999999999999999999999876443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=93.13  E-value=0.12  Score=45.47  Aligned_cols=43  Identities=28%  Similarity=0.591  Sum_probs=36.6

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      +|+.++.+|+||||+|.+.+.++.+++ +...|.++.+.+.+..
T Consensus       135 ~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  135 KDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             ccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeee
Confidence            577888999999999999999999999 6667888888776543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=92.54  E-value=0.91  Score=31.56  Aligned_cols=55  Identities=16%  Similarity=0.366  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           67 SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        67 ~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .++-+||+..|.+|.. +  +|+.|+     .|| ||.|.+.++|++|....+...+-...|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4677999999999864 3  344443     233 89999999999999998888877766654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=92.52  E-value=0.22  Score=37.76  Aligned_cols=41  Identities=22%  Similarity=0.306  Sum_probs=32.8

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIP   45 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~   45 (314)
                      .|...+|-|||.|++..+|.+|+..+  ..+..+.+.|-...+
T Consensus        52 ~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   52 NTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             CccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            57788999999999999999999943  466777777765444

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=92.24  E-value=0.19  Score=48.71  Aligned_cols=44  Identities=23%  Similarity=0.511  Sum_probs=36.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccC--ccCCcEEEEeecC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTI   44 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~--~i~g~~i~v~~~~   44 (314)
                      |++..|.-.+.|+||++++.++|.+||+.+|  +|.++.|.|+.+.
T Consensus       438 VTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  438 VTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             eecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            3455566778999999999999999999665  8899999997653

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=91.56  E-value=2.5  Score=42.81  Aligned_cols=61  Identities=8%  Similarity=0.132  Sum_probs=47.0

Q ss_pred             CCCCHHHHHHHHhccCCe-----EEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           66 SSVNEDEFKDFFMQFGDV-----QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        66 ~~~~e~~l~~~F~~~G~v-----~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ..++..+|..++.....|     -.|+|..+        |.||+... +.+++.++.|++..+.+++|.|+.+..
T Consensus       497 ~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~--------~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        497 DGVEVRHIVGAIANEGDISSRYIGNIKLFAS--------HSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             cCCCHHHHHHHHHhhcCCChhhCCcEEEeCC--------ceEEEcCh-hhHHHHHHHhccccccCCceEEEECCC
Confidence            457888888888766544     36777755        88998855 457788888999999999999998753

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

Probab=91.24  E-value=0.38  Score=36.19  Aligned_cols=28  Identities=21%  Similarity=0.394  Sum_probs=24.6

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHc
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIED   29 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~   29 (314)
                      .|-.|..+.|||||-|.++++|.+..+.
T Consensus        37 iDf~~~~N~GYAFVNf~~~~~~~~F~~~   64 (97)
T PF04059_consen   37 IDFKNKCNLGYAFVNFTSPQAAIRFYKA   64 (97)
T ss_pred             eeccCCCceEEEEEEcCCHHHHHHHHHH
Confidence            3667889999999999999999988874

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

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=89.98  E-value=1.4  Score=39.27  Aligned_cols=58  Identities=16%  Similarity=0.194  Sum_probs=41.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCCh-------HHHHHHHHhcC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-------QAVDDLLAKGN  119 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~-------~~a~~a~~~l~  119 (314)
                      ..|+|.|||.++...||+..+.+.+.+. +.|.-   . -+++-||+.|.+.       +++++++..++
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~p-m~isw---k-g~~~k~flh~~~~~~~~~~~~~~~~~~~s~~  395 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTP-MSISW---K-GHFGKCFLHFGNRKGVPSTQDDMDKVLKSLN  395 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCc-eeEee---e-cCCcceeEecCCccCCCCCchHHHHHhccCC
Confidence            4699999999999999999998875432 22221   1 2466899999663       46666666554

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=89.32  E-value=0.68  Score=41.15  Aligned_cols=36  Identities=28%  Similarity=0.574  Sum_probs=29.2

Q ss_pred             CCcceEEEcCCCCC------------CCHHHHHHHHhccCCeEEEEEe
Q 021295           54 FKTKKIFVGGIPSS------------VNEDEFKDFFMQFGDVQEHQIM   89 (314)
Q Consensus        54 ~~~~~l~V~nLp~~------------~~e~~l~~~F~~~G~v~~v~i~   89 (314)
                      ..+.+|++..||-.            .+|+.|+..|+.||.|..|+|+
T Consensus       147 erpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdip  194 (445)
T KOG2891|consen  147 ERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIP  194 (445)
T ss_pred             CCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCc
Confidence            35678999988843            3678899999999999888776

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=88.67  E-value=1.2  Score=31.16  Aligned_cols=63  Identities=17%  Similarity=0.331  Sum_probs=45.4

Q ss_pred             HHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           71 DEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        71 ~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|++.|...| +|..|.-+..+.+..+--.-||+++...+..++   ++-..|+++.|+|+....+
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~i---~~Ik~l~~~~V~vE~~~k~   65 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKEI---YKIKTLCGQRVKVERPRKR   65 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccce---eehHhhCCeEEEEecCCCC
Confidence            57888888877 577787777776777777888998877664443   3345678888888876544

These proteins are possibly involved in RNA binding or single strand DNA binding.

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=88.24  E-value=1.2  Score=31.02  Aligned_cols=63  Identities=14%  Similarity=0.165  Sum_probs=45.9

Q ss_pred             HHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           71 DEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        71 ~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|++.|++.| +|..|.-+..+.+..+--.-+|+.....+...   .|+-..|+++.|.|+.....
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~k~   65 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPHKR   65 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCccc
Confidence            47888898888 57888888887777777778888877655444   33445678888888765543

>KOG4213 consensus RNA-binding protein La [RNA processing and modification]

Probab=87.33  E-value=0.84  Score=37.97  Aligned_cols=60  Identities=13%  Similarity=0.176  Sum_probs=38.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC-CCcceEEEEEeCChHHHHHHHHh
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFDTEQAVDDLLAK  117 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~-g~~rG~afV~F~~~~~a~~a~~~  117 (314)
                      +..+++|..  +.+...++|.++.+  ++++.|.+-+.... -..+|-.||+|.+.+.+.++++.
T Consensus       109 ~~~r~v~~K--~td~ql~~l~qw~~--~k~~nv~mr~~~~k~~~fkGsvkv~f~tk~qa~a~~~~  169 (205)
T KOG4213|consen  109 IKERTVYKK--ITDDQLDDLNQWAS--GKGHNVKMRRHGNKAHPFKGSVKVTFQTKEQAFANDDT  169 (205)
T ss_pred             HHHhhhhcc--CCHHHHHHHHHHhc--ccceEeeccccCCCCCCCCCceEEEeecHHHHHhhhhh
Confidence            345667765  22333344444444  67877776654322 24678899999999999998876

>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=86.81  E-value=1.3  Score=32.26  Aligned_cols=36  Identities=6%  Similarity=0.268  Sum_probs=25.1

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      +.+-|.|.|.+.+.|+.|.+  +..++-+..|.|....
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            45789999999999999999  4457888888888754

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

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=86.22  E-value=0.38  Score=46.73  Aligned_cols=24  Identities=29%  Similarity=0.553  Sum_probs=21.6

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHc
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIED   29 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~   29 (314)
                      .+.++||.|++|++..+|++|+++
T Consensus       101 ~ggtkG~lf~E~~~~~~A~~aVK~  124 (698)
T KOG2314|consen  101 EGGTKGYLFVEYASMRDAKKAVKS  124 (698)
T ss_pred             cCCeeeEEEEEecChhhHHHHHHh
Confidence            344999999999999999999995

>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=85.10  E-value=2.2  Score=33.25  Aligned_cols=44  Identities=14%  Similarity=0.418  Sum_probs=25.7

Q ss_pred             CHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCCh-HHHHHHH
Q 021295           69 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-QAVDDLL  115 (314)
Q Consensus        69 ~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~-~~a~~a~  115 (314)
                      +.++|++.|+.|..++ |+.+.++.  -+.++|+|+|.+. .-.+.|+
T Consensus        30 ~~~~l~~~l~~f~p~k-v~~l~~~~--gh~g~aiv~F~~~w~Gf~~A~   74 (116)
T PF03468_consen   30 SNEELLDKLAEFNPLK-VKPLYGKQ--GHTGFAIVEFNKDWSGFKNAM   74 (116)
T ss_dssp             -SHHHHHHHHH---SE-EEEEEETT--EEEEEEEEE--SSHHHHHHHH
T ss_pred             CHHHHHHHHHhcCCce-eEECcCCC--CCcEEEEEEECCChHHHHHHH
Confidence            5589999999998775 55555533  4789999999764 3333333

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.

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

Probab=83.82  E-value=2.1  Score=38.45  Aligned_cols=83  Identities=12%  Similarity=0.342  Sum_probs=60.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCC-------CCCcceEEEEEeCChHHHHH----HHHhcCC
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS-------TSRSRGFGFITFDTEQAVDD----LLAKGNK  120 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~-------~g~~rG~afV~F~~~~~a~~----a~~~l~~  120 (314)
                      ++..++.|.+.||..+++-.++.+.|.+|++|+.|.++.+..       ..+..-.+.+.|-+.+.+..    .+++|+.
T Consensus        11 D~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsE   90 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSE   90 (309)
T ss_pred             ccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHH
Confidence            456788999999999999999999999999999999998751       22234567889988876644    3333332


Q ss_pred             --eeeCCeEEEEeecC
Q 021295          121 --LELAGAQVEVKKAE  134 (314)
Q Consensus       121 --~~~~gr~l~V~~a~  134 (314)
                        ..+....|.|.+..
T Consensus        91 fK~~L~S~~L~lsFV~  106 (309)
T PF10567_consen   91 FKTKLKSESLTLSFVS  106 (309)
T ss_pred             HHHhcCCcceeEEEEE
Confidence              33556666666544

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

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=83.09  E-value=24  Score=32.65  Aligned_cols=8  Identities=13%  Similarity=0.455  Sum_probs=3.9

Q ss_pred             HHHHHHHh
Q 021295           71 DEFKDFFM   78 (314)
Q Consensus        71 ~~l~~~F~   78 (314)
                      ++|.+.|.
T Consensus       243 ~ei~~~~~  250 (465)
T KOG3973|consen  243 EEIQSILS  250 (465)
T ss_pred             HHHHHHHH
Confidence            44555553

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=82.35  E-value=1.3  Score=36.97  Aligned_cols=75  Identities=23%  Similarity=0.267  Sum_probs=51.3

Q ss_pred             ceEEEcCCCCCCCH-----HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe-EEEE
Q 021295           57 KKIFVGGIPSSVNE-----DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA-QVEV  130 (314)
Q Consensus        57 ~~l~V~nLp~~~~e-----~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr-~l~V  130 (314)
                      .+|++.+|+..+-.     ...+.+|.++-+++...+++      +....-|.|.+++.|..|..+++...|.++ .++.
T Consensus        11 ~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lr------sfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~   84 (193)
T KOG4019|consen   11 TAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLR------SFRRVRINFSNPEAAADARIKLHSTSFNGKNELKL   84 (193)
T ss_pred             ceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHH------hhceeEEeccChhHHHHHHHHhhhcccCCCceEEE
Confidence            45666667665422     23345566655555544443      244678999999999999999999999988 7777


Q ss_pred             eecCCCC
Q 021295          131 KKAEPKK  137 (314)
Q Consensus       131 ~~a~~~~  137 (314)
                      -+|.+..
T Consensus        85 yfaQ~~~   91 (193)
T KOG4019|consen   85 YFAQPGH   91 (193)
T ss_pred             EEccCCC
Confidence            6666543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=82.27  E-value=2.9  Score=36.92  Aligned_cols=43  Identities=12%  Similarity=0.326  Sum_probs=36.1

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      .++++.|.|-|+|+..++|++||+  +...++++.|.+....+..
T Consensus       119 ~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~  163 (243)
T KOG0533|consen  119 RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPS  163 (243)
T ss_pred             CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcc
Confidence            488999999999999999999999  5567889998887765443

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length

Probab=80.93  E-value=2.7  Score=38.68  Aligned_cols=57  Identities=9%  Similarity=0.129  Sum_probs=37.0

Q ss_pred             EEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295           13 GFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus        13 aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      |||+|+++++|+.|++.....+.+.+.++.+.          +++.|+=.||..+..+..++.++..
T Consensus         1 aFVtF~~~~~a~~~~q~~~~~~~~~~~v~~AP----------eP~DI~W~NL~~~~~~r~~R~~~~~   57 (325)
T PF02714_consen    1 AFVTFNSQKSAQIALQLLLSKRPNSWRVSPAP----------EPDDIIWENLSISSKQRFLRRIIVN   57 (325)
T ss_pred             CEEEECCHHHHHHHHHHHhcCCCCCceEeeCC----------CcccccccccCCChHHHHHHHHHHH
Confidence            79999999999999995444444444544433          2344555777666666666655443

; GO: 0016020 membrane

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	314
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-26
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-18
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-18
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		5e-18
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-17
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-17
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-17
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-13
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-07
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-13
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-12
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		1e-11
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-10
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		9e-10
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-09
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		1e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-09
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-09
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-09
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		5e-09
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		8e-09
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		9e-09
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-09
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-08
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-07
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-07
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-07
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-07
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-07
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-07
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-07
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		3e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-07
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		4e-07
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		6e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		9e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		9e-07
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-06
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-06
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		3e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		5e-06
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		5e-06
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		6e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		6e-06
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		8e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		9e-06
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		1e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		3e-05
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		4e-05
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		7e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		8e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		1e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		1e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		1e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-04
3d2w_A	89	Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Co		4e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-04
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		5e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		8e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score =  114 bits (286), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 59/136 (43%), Positives = 91/136 (66%), Gaps = 5/136 (3%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
           MKD  TG+ RGFGF+++  PS VD+V++  HI++GK ++ KR IP+     +  KT KIF
Sbjct: 36  MKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR----DEQDKTGKIF 91
Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           VGGI   V   EF++FF Q+G + + Q+M D  T +SRGFGF+T+D+  AV D + +   
Sbjct: 92  VGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV-DRVCQNKF 150
Query: 121 LELAGAQVEVKKAEPK 136
           ++    ++E+K+AEP+
Sbjct: 151 IDFKDRKIEIKRAEPR 166

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 88.6 bits (218), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 14/155 (9%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE     PK AV  +D      
Sbjct: 46  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 100
Query: 54  -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
               KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 160
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
            ++ +     + G   EV+KA  K+      S +R
Sbjct: 161 KIVIQKYHT-VNGHNCEVRKALSKQEMASASSSQR 194

>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 = 88.6 bits (218), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 14/155 (9%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE     PK AV  +D      
Sbjct: 47  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 101
Query: 54  -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
               KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD
Sbjct: 102 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 161
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
            ++ +     + G   EV+KA  K+      S +R
Sbjct: 162 KIVIQKYHT-VNGHNCEVRKALSKQEMASASSSQR 195

>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 = 88.6 bits (218), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 14/155 (9%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE     PK AV  +D      
Sbjct: 45  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 99
Query: 54  -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
               KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD
Sbjct: 100 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 159
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
            ++ +     + G   EV+KA  K+      S +R
Sbjct: 160 KIVIQKYHT-VNGHNCEVRKALSKQEMASASSSQR 193

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 54/145 (37%), Positives = 77/145 (53%), Gaps = 14/145 (9%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE     PK AV  +D      
Sbjct: 46  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 100
Query: 54  -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
               KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 160
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
            ++ +     + G   EV+KA  K+
Sbjct: 161 KIVIQKYHT-VNGHNCEVRKALSKQ 184

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 54/145 (37%), Positives = 77/145 (53%), Gaps = 14/145 (9%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE     PK AV  +D      
Sbjct: 39  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 93
Query: 54  -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
               KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD
Sbjct: 94  HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 153
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
            ++ +     + G   EV+KA  K+
Sbjct: 154 KIVIQKYHT-VNGHNCEVRKALSKQ 177

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 54/145 (37%), Positives = 77/145 (53%), Gaps = 14/145 (9%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE     PK AV  +D      
Sbjct: 44  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 98
Query: 54  -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
               KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD
Sbjct: 99  HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 158
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
            ++ +     + G   EV+KA  K+
Sbjct: 159 KIVIQKYHT-VNGHNCEVRKALSKQ 182

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/119 (32%), Positives = 67/119 (56%), Gaps = 8/119 (6%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
           ++D+ TGQ  G+GFV Y+DP+  DK I   + +NG +++ K   +      S   +   +
Sbjct: 37  VRDKITGQSLGYGFVNYSDPNDADKAI---NTLNGLKLQTKTIKVSYARPSSASIRDANL 93
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
           +V G+P ++++ E +  F Q+G +   +I+ D +T  SRG GFI FD     E+A+  L
Sbjct: 94  YVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
           D KT  + V  +P ++ +DEFK  F   GD++  +++RD  T +S G+GF+ +      D
Sbjct: 2   DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNL 140
             +   N L+L    ++V  A P   ++
Sbjct: 61  KAINTLNGLKLQTKTIKVSYARPSSASI 88

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/87 (44%), Positives = 55/87 (63%), Gaps = 1/87 (1%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGGIP +  E E +++F +FG V E  ++ D    R RGFGFITF+ EQ+VD  +  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
            +  ++ G +VEVK+AEP+      PS
Sbjct: 72  -HFHDIMGKKVEVKRAEPRDSKSSGPS 97

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/119 (31%), Positives = 63/119 (52%), Gaps = 8/119 (6%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
           ++D+ TGQ  G+GFV Y DP   +K I   + +NG +++ K   +      S   +   +
Sbjct: 35  VRDKITGQSLGYGFVNYIDPKDAEKAI---NTLNGLRLQTKTIKVSYARPSSASIRDANL 91
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
           +V G+P ++ + E +  F Q+G +   +I+ D  T  SRG GFI FD     E+A+  L
Sbjct: 92  YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 8/86 (9%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           + V  +P ++ ++EF+  F   G+++  +++RD  T +S G+GF+ +    D E+A++ L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 115 LAKGNKLELAGAQVEVKKAEPKKPNL 140
               N L L    ++V  A P   ++
Sbjct: 65  ----NGLRLQTKTIKVSYARPSSASI 86

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 5/97 (5%)
Query: 44  IPKGA-VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF 102
           +P+G+ +GS   K   +F+GG+     ++  +++F QFG+V+E  +MRD  T RSRGFGF
Sbjct: 15  VPRGSHMGSSGCK---MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 103 ITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
           +TF  +  VD +LA+ ++ EL    ++ K A P++  
Sbjct: 72  VTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRRAQ 107

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+     ++  +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 118 GNKLELAGAQVEVKKA 133
            ++ EL    ++ K A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 60.8 bits (146), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 74/150 (49%), Gaps = 14/150 (9%)
Query: 3   DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR---------TIPKGAVGS 51
           D  T + +GF FV Y  P      +E  ++ ++ G+ +++ R          I + A  +
Sbjct: 63  DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 122
Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           + F   +I+V  +   +++D+ K  F  FG ++   + RD +T + +G+GFI ++  Q+ 
Sbjct: 123 RAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 112 DDLLAKGNKLELAGAQVEVKKA-EPKKPNL 140
            D ++  N  +L G  + V KA  P  P L
Sbjct: 181 QDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 73/150 (48%), Gaps = 14/150 (9%)
Query: 3   DRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKR---------TIPKGAVGS 51
           D  T + +GF FV Y  P      +E  +  ++ G+ +++ R          I + A  +
Sbjct: 48  DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 107
Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           + F   +I+V  +   +++D+ K  F  FG ++   + RD +T + +G+GFI ++  Q+ 
Sbjct: 108 RAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 112 DDLLAKGNKLELAGAQVEVKKA-EPKKPNL 140
            D ++  N  +L G  + V KA  P  P L
Sbjct: 166 QDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 195

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 73/150 (48%), Gaps = 14/150 (9%)
Query: 3   DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR---------TIPKGAVGS 51
           D  T + +GF FV Y  P      +E  ++  + G+ +++ R          I + A  +
Sbjct: 47  DSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEA 106
Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           + F   +I+V  +   +++D+ K  F  FG ++   + RD +T + +G+GFI ++  Q+ 
Sbjct: 107 RAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 112 DDLLAKGNKLELAGAQVEVKKA-EPKKPNL 140
            D ++  N  +L G  + V KA  P  P L
Sbjct: 165 QDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 45/87 (51%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVGG+    NE   +  F ++G + E  +++D  T RSRGFGF+TF+      D +  
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
            N   + G Q+ V +A     N   PS
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNRSGPS 100

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 52/88 (59%), Gaps = 1/88 (1%)
Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           +K+F+GG+     E+  ++++ Q+G + +  +MRD ++ RSRGFGF+TF +   VD  +A
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 117 KGNKLELAGAQVEVKKAEPKKPNLPQPS 144
                 + G  VE K+A  ++ +   PS
Sbjct: 88  -ARPHSIDGRVVEPKRAVAREESGSGPS 114

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 64/129 (49%), Gaps = 5/129 (3%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
           M+D KTG   G+ FV +       + I+   ++NG  V  KR  +     G +  K   +
Sbjct: 36  MRDYKTGYSYGYAFVDFTSEMDSQRAIK---VLNGITVRNKRLKVSYARPGGESIKDTNL 92
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKG 118
           +V  +P ++ +D+    F ++G + +  I+RD  T R RG  F+ ++  E+A + + A  
Sbjct: 93  YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Query: 119 NKLELAGAQ 127
           N +   G+Q
Sbjct: 153 NVIPEGGSQ 161

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVGG+  S  ++  + +F Q+G+V +  IM+D +T++SRGFGF+ F     V  +LA 
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 118 GNKLELAGAQVEVKKAEPK 136
                L G  ++ K   P+
Sbjct: 78  -RPHTLDGRNIDPKPCTPR 95

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFVGG+  +   ++ K +F QFG V +  +M D +T+R RGFGF+TF++E  V+  + + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 119 NKLELAGAQVEVKKA 133
           +  E+    VE KKA
Sbjct: 61  HFHEINNKMVECKKA 75

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 57.8 bits (138), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/120 (24%), Positives = 60/120 (50%), Gaps = 4/120 (3%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
           ++D+  G   G+GFV Y      ++ I   + +NG +++ K   +      S+  K   +
Sbjct: 35  IRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSKTIKVSYARPSSEVIKDANL 91
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           ++ G+P ++ + + +D F +FG +   +++ D +T  SRG  FI FD     ++ +   N
Sbjct: 92  YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           + V  +P ++ +DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 115 LAKGNKLELAGAQVEVKKAEP 135
               N L L    ++V  A P
Sbjct: 65  ----NGLRLQSKTIKVSYARP 81

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 57.8 bits (138), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/120 (24%), Positives = 60/120 (50%), Gaps = 4/120 (3%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
           ++D+  G   G+GFV Y      ++ I   + +NG +++ K   +      S+  K   +
Sbjct: 35  IRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSKTIKVSYARPSSEVIKDANL 91
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           ++ G+P ++ + + +D F +FG +   +++ D +T  SRG  FI FD     ++ +   N
Sbjct: 92  YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           + V  +P ++ +DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 115 LAKGNKLELAGAQVEVKKAEP 135
               N L L    ++V  A P
Sbjct: 65  ----NGLRLQSKTIKVSYARP 81

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +++VG +  ++ ED  +  F  FG ++  Q+M D  T RS+G+GFITF   +     L +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 118 GNKLELAGAQVEV 130
            N  ELAG  ++V
Sbjct: 88  LNGFELAGRPMKV 100

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 10/104 (9%)
Query: 47  GAVGSKDFKTKK--IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
           G+ GS    T K  ++VGG+   V++      F+ FGD+ + QI  D+ T + RGF F+ 
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 105 F----DTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
           F    D   A+D++    N+ EL G  + V  A+P +     PS
Sbjct: 61  FELAEDAAAAIDNM----NESELFGRTIRVNLAKPMRIKESGPS 100

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           KD    KIFVGG+P    +   + +F  FGD++E  ++ D  T +SRG+GF+T     A 
Sbjct: 13  KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 112 D 112
           +
Sbjct: 73  E 73

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K FVGG+    ++ + KD+F +FG+V +  I  D +T RSRGFGFI F    +V+ +L +
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 118 GNKLELAGAQVEVKKA 133
             +  L G  ++ KKA
Sbjct: 73  -KEHRLDGRVIDPKKA 87

>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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
            KKIFVGG+     E++ +++F  FG+V+  ++  D+ T++ RGF FITF  E+ V  ++
Sbjct: 1   VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 116 AKG-NKLELAGAQVEV 130
            K  + + L+  +++V
Sbjct: 61  EKKYHNVGLSKCEIKV 76

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 66/135 (48%), Gaps = 13/135 (9%)
Query: 5   KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFK----TKKI 59
           +  Q + F F+ +       + +  D  I  G+ ++I+R          D++      K+
Sbjct: 48  QINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR--------PHDYQPLPGAHKL 99
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           F+GG+P+ +N+D+ K+    FG ++   +++D +T  S+G+ F  +      D  +A  N
Sbjct: 100 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 159
Query: 120 KLELAGAQVEVKKAE 134
            ++L   ++ V++A 
Sbjct: 160 GMQLGDKKLLVQRAS 174

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 66/135 (48%), Gaps = 13/135 (9%)
Query: 5   KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFK----TKKI 59
           +  Q + F F+ +       + +  D  I  G+ ++I+R          D++      K+
Sbjct: 46  QINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR--------PHDYQPLPGAHKL 97
Query: 60  FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
           F+GG+P+ +N+D+ K+    FG ++   +++D +T  S+G+ F  +      D  +A  N
Sbjct: 98  FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Query: 120 KLELAGAQVEVKKAE 134
            ++L   ++ V++A 
Sbjct: 158 GMQLGDKKLLVQRAS 172

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
           D KT  + V  +P ++ +DEFK  F   GD++  +++RD  T +S G+GF+ +      D
Sbjct: 2   DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNL 140
             +   N L+L    ++V  A P   ++
Sbjct: 61  KAINTLNGLKLQTKTIKVSYARPSSASI 88

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 45/77 (58%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+P+ +N+D+ K+    FG ++   +++D +T  S+G+ F  +      D  +A 
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 118 GNKLELAGAQVEVKKAE 134
            N ++L   ++ V++A 
Sbjct: 176 LNGMQLGDKKLLVQRAS 192

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%)
Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           +  ++VG +  ++ ED  +  F  FG +    +M+D  T RS+G+GFITF   +     L
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
            + N  ELAG  + V     +      PS
Sbjct: 65  EQLNGFELAGRPMRVGHVTERLDGGSGPS 93

>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 = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           + I+VG +  S   ++ K+ F QFG V   +++ D  T + +GFGF+    E++V + +A
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 117 KGNKLELAGAQVEVKKAEPKK 137
           K +  +  G  + V +A PKK
Sbjct: 61  KLDNTDFMGRTIRVTEANPKK 81

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 45/76 (59%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+P+ +N+D+ K+    FG ++   +++D +T  S+G+ F  +      D  +A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 118 GNKLELAGAQVEVKKA 133
            N ++L   ++ V++A
Sbjct: 63  LNGMQLGDKKLLVQRA 78

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 45/86 (52%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++VGG+   V+E    + F+Q G V    + +D  T + +G+GF+ F +E+  D  +   
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPS 144
           + ++L G  + V KA     NL  PS
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNLSGPS 103

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 3/90 (3%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+    NE   K  F + G + E  +++D  TS+SRGF FITF+      +    
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
            N   L G  ++V++A  KKP+      RR
Sbjct: 68  MNGKSLHGKAIKVEQA--KKPSFQSGGRRR 95

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +F+GG+     + + KD+F +FG+V +  +  D  T RSRGFGF+ F   ++VD ++ + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60
Query: 119 NKLELAGAQVEVKKA 133
            + +L G  ++ K+A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/144 (23%), Positives = 72/144 (50%), Gaps = 16/144 (11%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRT-----IPKGAVGSKD 53
            +D  T +  G+ +V +  P+  ++ ++  +  +I GK V I  +     + K  VG+  
Sbjct: 48  CRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN-- 105
Query: 54  FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
                IF+  +  S++     D F  FG++   +++ D + S+  G+GF+ F+T++A + 
Sbjct: 106 -----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAER 158
Query: 114 LLAKGNKLELAGAQVEVKKAEPKK 137
            + K N + L   +V V + + +K
Sbjct: 159 AIEKMNGMLLNDRKVFVGRFKSRK 182

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/144 (23%), Positives = 72/144 (50%), Gaps = 16/144 (11%)
Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRT-----IPKGAVGSKD 53
            +D  T +  G+ +V +  P+  ++ ++  +  +I GK V I  +     + K  VG+  
Sbjct: 43  CRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN-- 100
Query: 54  FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
                IF+  +  S++     D F  FG++   +++ D + S+  G+GF+ F+T++A + 
Sbjct: 101 -----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAER 153
Query: 114 LLAKGNKLELAGAQVEVKKAEPKK 137
            + K N + L   +V V + + +K
Sbjct: 154 AIEKMNGMLLNDRKVFVGRFKSRK 177

>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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           IFVGG+     E++ +++F  FG+V+  ++  D+ T++ RGF FITF  E+ V  ++ K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 119 -NKLELAGAQVEV 130
            + + L+  +++V
Sbjct: 62  YHNVGLSKCEIKV 74

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           +  +FVG     + EDE ++FF Q+GDV +  I +       R F F+TF  +Q    L 
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLC 59
Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
             G  L + G  V +  AEPK  +   PS
Sbjct: 60  --GEDLIIKGISVHISNAEPKHNSNSGPS 86

>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 = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +   +  ++ K  F  FG + + ++++D +T +S+G+GF++F  +   ++ + + 
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPSY 145
               L G Q+    A  +KP  P+ +Y
Sbjct: 78  GGQWLGGRQIRTNWAT-RKPPAPKSTY 103

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 49/85 (57%), Gaps = 6/85 (7%)
Query: 47  GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF- 105
           G +GS       +FVGGI   ++E E + FF ++G V+E +I+ D  T  S+G+GF++F 
Sbjct: 1   GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 59
Query: 106 ---DTEQAVDDLLA-KGNKLELAGA 126
              D ++ V+  +   G KL+L  A
Sbjct: 60  NDVDVQKIVESQINFHGKKLKLGPA 84

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 44/86 (51%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +FVG +   +  ++ K  F  FG + + ++++D +T +S+G+GF++F  +   ++ +   
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPS 144
               L G Q+    A  K P    PS
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPSGPS 103

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 41/85 (48%)
Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
           D   + +FVG IP    E++ KD F + G V   +++ D  T + +G+GF  +  ++   
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
             +   N  E +G  + V  A  +K
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEK 89

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           + V  +P ++ +DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 115 LAKGNKLELAGAQVEVKKAEP 135
               N L L    ++V  A P
Sbjct: 67  ----NGLRLQSKTIKVSYARP 83

>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 = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 47  GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           G+ G KD    K+F+G IP +++E + K  F +FG + E  +++D  T   +G  F+T+
Sbjct: 4   GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 54  FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQ 109
           F+   + V  +P +  +DE +  F   G+V+  +++RD     S G+GF+ +    D E+
Sbjct: 17  FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 110 AVDDLLAKGNKLELAGAQVEVKKAEP 135
           A++ L    N L L    ++V  A P
Sbjct: 77  AINTL----NGLRLQSKTIKVSYARP 98

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/85 (29%), Positives = 43/85 (50%)
Query: 50  GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
           GS     + ++VGG+   V++      F+ FGD+ + QI  D+ T + RGF F+ F+  +
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 110 AVDDLLAKGNKLELAGAQVEVKKAE 134
                +   N+ EL G  + V  A+
Sbjct: 61  DAAAAIDNMNESELFGRTIRVNLAK 85

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 20/77 (25%), Positives = 43/77 (55%)
Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           + + V  IP++V+E + +  F ++G ++  +I+ D  T +SRG+GF+ F +  +    +A
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 117 KGNKLELAGAQVEVKKA 133
             N   +   +++V  A
Sbjct: 103 GLNGFNILNKRLKVALA 119

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
           ++V G+P ++++ E +  F Q+G +   +I+ D +T  SRG GFI FD     E+A+  L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 52/92 (56%), Gaps = 5/92 (5%)
Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQ- 109
           D    K+FVG +P + +E + ++ F Q+G V E  ++RD S +  +S+G  F+TF T + 
Sbjct: 12  DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 110 AVDDLLAKGNKLELAGAQ--VEVKKAEPKKPN 139
           A++   A  N   L G    +++K A+ +K N
Sbjct: 72  ALEAQNALHNMKVLPGMHHPIQMKPADSEKNN 103

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           ++VGG+   V++      F+ FGD+ + QI  D+ T + RGF F+ F+  +     +   
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 119 NKLELAGAQVEVKKA 133
           N+ EL G  + V  A
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           +FVGGI   ++E E + FF ++G V+E +I+ D  T  S+G+GF++F    D ++ V+  
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 115 LA-KGNKLELAGA 126
           +   G KL+L  A
Sbjct: 71  INFHGKKLKLGPA 83

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           +FVGGI   ++E E + FF ++G V+E +I+ D  T  S+G+GF++F    D ++ V+  
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 115 LA-KGNKLELAGA 126
           +   G KL+L  A
Sbjct: 71  INFHGKKLKLGPA 83

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 112
           + ++VGG+   V++      F+ FGD+ + QI  D+ T + RGF F+ F    D   A+D
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 113 DLLAKGNKLELAGAQVEVKKA 133
           ++    N+ EL G  + V  A
Sbjct: 124 NM----NESELFGRTIRVNLA 140

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 5/87 (5%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQ-AVDDL 114
           K+FVG +P + +E + ++ F Q+G V E  ++RD S +  +S+G  F+TF T + A++  
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 115 LAKGNKLELAGAQ--VEVKKAEPKKPN 139
            A  N   L G    +++K A+ +K N
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNN 91

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 112
           + ++VGG+   V++      F+ FGD+ + QI  D+ T + RGF F+ F    D   A+D
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 113 DLLAKGNKLELAGAQVEVKKA 133
           ++    N+ EL G  + V  A
Sbjct: 66  NM----NESELFGRTIRVNLA 82

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           KT  + V G+P    E + K++F  FG+V   Q+ +D  T  S+GFGF+ F
Sbjct: 14  KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

>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 = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           KD    K+FVG IP  ++E + K  F +FG + E  +++D  T   +G  F+T+
Sbjct: 11  KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQAV 111
           K FVG +P + +E + ++ F Q+G V E  ++RD S +  +S+G  F+TF T +A 
Sbjct: 5   KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N 
Sbjct: 17  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 121 LELAGAQVEVKKAEPKKPN 139
           +EL G ++ V  +  K+P+
Sbjct: 77  MELDGRRIRVDFSITKRPH 95

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N 
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 121 LELAGAQVEVKKAEPKKPN 139
           +EL G ++ V  +  K+P+
Sbjct: 80  MELDGRRIRVDFSITKRPH 98

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/55 (38%), Positives = 36/55 (65%), Gaps = 2/55 (3%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQA 110
           K+FVG +P + +E + ++ F Q+G V E  ++RD S +  +S+G  F+TF T +A
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+G +P    E E +  F Q+G V E  I+++        +GF+  + + A +D +  
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
            +  +L G  + V+ ++ K      PS
Sbjct: 62  LHHYKLHGVNINVEASKNKSKASSGPS 88

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N 
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 121 LELAGAQVEVKKAEPKKPN 139
           +EL G ++ V  +  K+P+
Sbjct: 111 MELDGRRIRVDFSITKRPH 129

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/129 (22%), Positives = 62/129 (48%), Gaps = 8/129 (6%)
Query: 3   DRKTGQPRGFGFVTYADPSVVDKVIEDTHI-INGKQVEIKRTIPKGAVGSKDFKTKKIFV 61
           D + G  R FG+V +     ++K +E T + + G ++++++  PKG    K+   + +  
Sbjct: 41  DVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK--PKGKDSKKERDARTLLA 98
Query: 62  GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 121
             +P  V +DE K+ F    +++   + +D    +S+G  +I F TE   +    +    
Sbjct: 99  KNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFKTEADAEKTFEEKQGT 153
Query: 122 ELAGAQVEV 130
           E+ G  + +
Sbjct: 154 EIDGRSISL 162

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/117 (25%), Positives = 54/117 (46%), Gaps = 10/117 (8%)
Query: 5   KTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVE---IKRTIPKGAVGSKDFKTKKIFV 61
           K  +   + FV Y      +  ++    +NGKQ+E   +K      +  S    T  +FV
Sbjct: 36  KNNKNVNYAFVEYHQSHDANIALQ---TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFV 92
Query: 62  GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
           G +  +V+++  ++ F  F       +M D  T  SRG+GF++F    D + A+D +
Sbjct: 93  GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex Wit Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVG     +  +E + FF Q+G+V +  I +       R F F+TF  ++    L   
Sbjct: 13  KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLC-- 65
Query: 118 GNKLELAGAQVEVKKAEPKKPNL 140
           G  L + G  V +  AEPK   L
Sbjct: 66  GEDLIIKGISVHISNAEPKHNKL 88

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 50  GSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
           G K F  + ++FVG +P  + E+E +  F ++G   E  I +D      +GFGFI  +T 
Sbjct: 15  GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR 68
Query: 109 QAVDDLLAKGNKLELAGAQVEVK----KAEPKKPNLPQ 142
              +    + + + L G Q+ V+     A     NLPQ
Sbjct: 69  TLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQ 106

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 11/68 (16%)
Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++FVG +P+ + E++FK  F ++G+  E  I RD      RGFGFI  ++       LA+
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRT-----LAE 72
Query: 118 GNKLELAG 125
             K EL G
Sbjct: 73  IAKAELDG 80

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 1/87 (1%)
Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDV-QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           IF+G +   ++E    D F  FG + Q  +IMRD  T  S+G+ FI F +  A D  +  
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
            N   L    + V  A  K      PS
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSKGSGPS 94

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 36/70 (51%)
Query: 61  VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
           V G+     E + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N 
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 121 LELAGAQVEV 130
           +EL G ++ V
Sbjct: 80  MELDGRRIRV 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	314
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.95
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.94
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.94
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.94
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.94
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.94
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.93
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.93
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.93
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.93
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.93
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.91
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.91
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.9
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.9
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.89
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.88
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.88
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.88
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.88
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.88
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.88
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.87
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.87
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.86
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.86
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.85
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.84
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.84
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.84
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.84
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.84
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.84
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.83
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.83
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.83
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.83
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.83
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.83
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.83
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.82
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.82
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.82
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.82
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.82
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.82
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.82
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.82
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.82
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.82
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.81
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.81
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.81
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.81
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.81
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.81
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.81
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.81
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.81
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.81
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.81
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.8
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.8
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.8
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.8
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.8
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.8
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.79
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.79
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.78
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.78
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.78
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.78
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.78
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.78
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.78
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.77
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.77
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.77
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.77
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.77
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.77
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.77
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.76
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.76
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.76
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.76
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.75
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.75
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.75
1x5p_A	97	Negative elongation factor E; structure genomics,	99.75
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.75
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.75
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.74
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.74
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.74
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.74
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.73
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.73
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.73
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.73
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.72
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.72
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.72
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.72
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.71
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.71
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.71
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.7
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.7
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.69
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.68
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.66
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.66
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.66
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.64
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.63
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.63
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.62
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.61
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.59
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.57
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.56
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.56
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.55
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.54
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.54
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.51
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.51
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.49
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.43
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.4
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.22
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.21
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.09
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.04
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.03
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.78
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.74
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.64
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	98.62
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.59
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.56
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.54
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.52
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.52
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	98.5
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.5
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.48
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.48
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.47
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.46
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.46
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.45
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.45
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.45
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.44
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.44
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.44
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.44
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.44
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.43
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.43
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.43
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.42
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.42
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.41
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.41
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.41
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.41
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.4
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.39
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.38
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.38
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.38
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.38
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.36
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.35
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.35
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.34
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.34
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.33
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.32
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.32
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.32
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.32
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.31
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.31
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.31
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.3
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.3
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.3
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.3
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.29
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.29
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.29
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.28
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.27
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.27
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.27
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.27
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.27
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.27
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.27
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.27
2div_A	99	TRNA selenocysteine associated protein; structural	98.26
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.26
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.26
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.25
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.25
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.24
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.24
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.23
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.23
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.22
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.2
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.2
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.18
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.17
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.17
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.17
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.15
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.13
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.13
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.13
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.11
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.1
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.1
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	97.38
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.09
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.09
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.04
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.04
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.03
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.01
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.01
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	97.97
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.97
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.97
1x5o_A	114	RNA binding motif, single-stranded interacting pro	97.95
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	97.94
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	97.93
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	97.93
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	97.9
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	97.89
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	97.89
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	97.87
1x5p_A	97	Negative elongation factor E; structure genomics,	97.87
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	97.86
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	97.85
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	97.83
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	97.82
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	97.81
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	97.8
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	97.79
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	97.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	97.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	97.75
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	97.75
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	97.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	97.73
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	97.73
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	97.72
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	97.71
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	97.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	97.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.69
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.67
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	97.63
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	97.62
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	97.61
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	97.6
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	97.57
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.56
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	97.56
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	97.55
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	97.54
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	97.54
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	97.52
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	97.51
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	97.49
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	97.49
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	97.48
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	97.48
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	97.45
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	97.44
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	97.41
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.36
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	97.34
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	97.31
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	97.15
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	96.94
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	96.91
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.78
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	96.51
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.42
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	96.22
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.04
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	95.77
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.15
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	93.54
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.34
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	88.54
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	88.05
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	85.31
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	82.48

>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=99.95  E-value=3e-27  Score=200.73  Aligned_cols=139  Identities=37%  Similarity=0.676  Sum_probs=117.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCC--CCCCcceEEEcCCCCCCCHHHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGS--KDFKTKKIFVGGIPSSVNEDEFKDFF   77 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~--~~~~~~~l~V~nLp~~~~e~~l~~~F   77 (314)
                      |+|+.|++++|||||+|.+.++|++||+ +.+.+.++.|.|+++.+......  .....++|||.|||+++++++|+++|
T Consensus        46 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F  125 (196)
T 1l3k_A           46 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF  125 (196)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHH
T ss_pred             EEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHH
Confidence            4678899999999999999999999999 55689999999999876644332  34566899999999999999999999


Q ss_pred             hccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCC
Q 021295           78 MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  140 (314)
Q Consensus        78 ~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~  140 (314)
                      ++||+|+.|.|+.++.++++++||||+|+++++|++||+. ++..|+++.|.|.+|.++....
T Consensus       126 ~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          126 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             TTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC------
T ss_pred             hcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHhc
Confidence            9999999999999999999999999999999999999998 7899999999999999887654

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

Probab=99.94  E-value=7e-27  Score=201.45  Aligned_cols=141  Identities=25%  Similarity=0.503  Sum_probs=121.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC-------CCCCcceEEEcCCCCCCCHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS-------KDFKTKKIFVGGIPSSVNED   71 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~-------~~~~~~~l~V~nLp~~~~e~   71 (314)
                      |+|+.|+++++||||+|.+.++|++|++  +...|.++.|.|.++........       .....++|||.|||++++++
T Consensus        61 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~  140 (216)
T 2qfj_A           61 SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD  140 (216)
T ss_dssp             CCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHH
T ss_pred             eecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHH
Confidence            4678899999999999999999999998  45688999999988765532211       23456899999999999999


Q ss_pred             HHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCCC
Q 021295           72 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLP  141 (314)
Q Consensus        72 ~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~~  141 (314)
                      +|+++|++||+|+.|+|++++.++++++||||+|++.++|++||+.||+..|.+++|+|.++.++....+
T Consensus       141 ~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~~~  210 (216)
T 2qfj_A          141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL  210 (216)
T ss_dssp             HHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSSTTS
T ss_pred             HHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999998755443

>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=99.94  E-value=1.6e-27  Score=197.24  Aligned_cols=131  Identities=45%  Similarity=0.859  Sum_probs=120.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhcc
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQF   80 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~   80 (314)
                      |+|+.|++++|||||+|.++++|++|+++.+.+.++.|.++++.++..    ..+.++|||.|||+++++++|+++|++|
T Consensus        36 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~----~~~~~~l~V~nlp~~~t~~~l~~~F~~~  111 (167)
T 2cjk_A           36 MKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE----QDKTGKIFVGGIGPDVRPKEFEEFFSQW  111 (167)
T ss_dssp             CCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHH----HHHCEEEEEEEECTTCCHHHHHHHHHTT
T ss_pred             EECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhh----ccCCCeEEECCCCCCCCHHHHHHHHHhC
Confidence            567889999999999999999999999988889999999988765432    2346799999999999999999999999


Q ss_pred             CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           81 GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        81 G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      |+|+.|.|+.++.++++++||||+|+++++|++|++ ++...|.+++|+|++|.++
T Consensus       112 G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          112 GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             SCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             ccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999999999999899999999999999999999998 7999999999999999876

>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=99.94  E-value=7.9e-26  Score=186.28  Aligned_cols=133  Identities=20%  Similarity=0.286  Sum_probs=108.7

Q ss_pred             CcccEEEEEECCHHHHHHHHHccC---ccCCcEE------EEeecC--CCCCCCCCCCCcceEEEcCCCCCCCHHHHHHH
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDTH---IINGKQV------EIKRTI--PKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDF   76 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~~---~i~g~~i------~v~~~~--~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~   76 (314)
                      +++|||||+|.+.++|++|++..+   .+++...      ......  ............++|||+|||++++|++|+++
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~   90 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRV   90 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            699999999999999999997322   2222221      111111  11222234456789999999999999999999


Q ss_pred             HhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCC
Q 021295           77 FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  140 (314)
Q Consensus        77 F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~  140 (314)
                      |++||+|++|.|++|+.++++++||||+|++.++|++||+.||+..|.+++|+|+++.++.+..
T Consensus        91 F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  154 (158)
T 2kn4_A           91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  154 (158)
T ss_dssp             HHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCCC
T ss_pred             HHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999875543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.94  E-value=1.7e-25  Score=184.49  Aligned_cols=131  Identities=21%  Similarity=0.419  Sum_probs=118.1

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      +|+ ++++++||||+|.+.++|++|++  +...+.++.|.++++.+...  ....+.++|||.|||+++++++|+++|++
T Consensus        34 ~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~--~~~~~~~~l~v~nl~~~~t~~~l~~~f~~  110 (166)
T 3md3_A           34 IDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ--SSSDDTFNLFVGDLNVNVDDETLRNAFKD  110 (166)
T ss_dssp             CCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC--CCCTTCEEEEEESCCTTCCHHHHHHHHTT
T ss_pred             ECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC--CCCCCCceEEECCCCCCCCHHHHHHHHhc
Confidence            444 57899999999999999999996  55688999999998876544  34556789999999999999999999999


Q ss_pred             cCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           80 FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        80 ~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ||+|+.|.|+.++.++++++||||+|+++++|++|++.||+..|.+++|+|++|++
T Consensus       111 ~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          111 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             STTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             cCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999999999999999999999999999999999999999999999999999863

>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=99.94  E-value=9.5e-26  Score=186.61  Aligned_cols=129  Identities=23%  Similarity=0.546  Sum_probs=118.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+|+.|++++|||||+|.++++|++|++  +...+.++.|.|+++.+...    ..+.++|||.|||.++++++|+++|+
T Consensus        36 ~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~  111 (168)
T 1b7f_A           36 MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE----SIKDTNLYVTNLPRTITDDQLDTIFG  111 (168)
T ss_dssp             CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS----TTTTCEEEEESCCTTCCHHHHHHHHT
T ss_pred             EEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc----cCCCCCEEEeCCCCCCCHHHHHHhhh
Confidence            4577899999999999999999999997  55688999999999876543    34678999999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEeec
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVKKA  133 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~~a  133 (314)
                      +||+|+.|.|++++.++++++||||+|+++++|++|++.||+..|.+  ++|+|++|
T Consensus       112 ~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          112 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             cCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999998899999999999999999999999999999987  99999876

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.93  E-value=2.5e-26  Score=198.56  Aligned_cols=134  Identities=23%  Similarity=0.496  Sum_probs=117.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+|+.|++++|||||+|.+.++|++||+  +...+.++.|.+.++......  .....++|||.|||++++|++|+++|+
T Consensus        48 ~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~--~~~~~~~l~v~nl~~~~t~~~l~~~F~  125 (213)
T 4f02_A           48 CRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSL--RKSGVGNIFIKNLDKSIDNKALYDTFS  125 (213)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHH--HHHCTTEEEEESCCTTCCHHHHHHHHG
T ss_pred             ecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccccc--cccccccceECCcccccHHHHHHHHHh
Confidence            4688999999999999999999999998  455788999998877654322  223457899999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      +||+|++|+|++|.  ..+++||||+|+++++|++||+.||+..|.+++|+|++|.+++.
T Consensus       126 ~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          126 AFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             GGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHHH
T ss_pred             hcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCcc
Confidence            99999999999985  34799999999999999999999999999999999999987643

>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=99.93  E-value=6.8e-26  Score=188.34  Aligned_cols=127  Identities=23%  Similarity=0.488  Sum_probs=114.9

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD   82 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~   82 (314)
                      ..+.++|+||||+|.++++|++|++ +...+.++.|.|+++.+...    ....++|||.|||+++++++|+++|++||+
T Consensus        45 ~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~~----~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~  120 (172)
T 2g4b_A           45 VQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQP----LPGAHKLFIGGLPNYLNDDQVKELLTSFGP  120 (172)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEECEEECCSSCCC----CTTTTCEEEECCCTTCCHHHHHHHHHTTSC
T ss_pred             eEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceeeecCCcccCC----CCCCCEEEEEcCCCcCCHHHHHHHHHhcCC
Confidence            3467889999999999999999996 45688999999988655432    345789999999999999999999999999


Q ss_pred             eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           83 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        83 v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      |+.|.|++++.++++++||||+|+++++|++|++.||+..|.+++|+|++|.
T Consensus       121 v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          121 LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999999999899999999999999999999999999999999999999874

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.93  E-value=7.9e-26  Score=192.22  Aligned_cols=136  Identities=21%  Similarity=0.449  Sum_probs=119.6

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC----------------CCCCCcceEEEcCCC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG----------------SKDFKTKKIFVGGIP   65 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~----------------~~~~~~~~l~V~nLp   65 (314)
                      +..++++|+||||+|.++++|++||+ +...|.++.|.|+++.+.....                ......++|||.|||
T Consensus        44 ~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  123 (198)
T 2yh0_A           44 AVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP  123 (198)
T ss_dssp             EEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCC
T ss_pred             EeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCC
Confidence            34567899999999999999999996 4458899999999876543221                122466899999999


Q ss_pred             CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           66 SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        66 ~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      +++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++|++.||+..|.+++|+|+++.++..
T Consensus       124 ~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             TTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999999999999999999999999998999999999999999999999999999999999999999987653

>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=99.93  E-value=2.2e-25  Score=183.90  Aligned_cols=129  Identities=31%  Similarity=0.610  Sum_probs=116.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFM   78 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~   78 (314)
                      |+|+.|+++++||||+|.++++|++|++  +...+.++.|.|.++.+...    ....++|||.|||+++++++|+++|+
T Consensus        35 ~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~  110 (167)
T 1fxl_A           35 VRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA----SIRDANLYVSGLPKTMTQKELEQLFS  110 (167)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG----GGTTCEEEEESCCTTCCHHHHHHHHG
T ss_pred             EeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc----cCCCCcEEECCCCCcCCHHHHHHHHH
Confidence            3577799999999999999999999998  55688999999998876533    34568999999999999999999999


Q ss_pred             ccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE--EEEeec
Q 021295           79 QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ--VEVKKA  133 (314)
Q Consensus        79 ~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~--l~V~~a  133 (314)
                      +||+|+.|+|+.++.++++++||||+|+++++|++|++.||+..|.++.  |+|++|
T Consensus       111 ~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             hcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999889999999999999999999999999999999965  888775

>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=99.93  E-value=1.3e-25  Score=187.36  Aligned_cols=129  Identities=20%  Similarity=0.412  Sum_probs=115.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      |+|+.|+++||||||+|.++++|++|++ +...+.++.|.|+++.++..  ....+.++|||.|||+++++++|+++|++
T Consensus        45 ~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~--~~~~~~~~l~v~nlp~~~t~~~l~~~F~~  122 (175)
T 1fje_B           45 VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDS--KKVRAARTLLAKNLSFNITEDELKEVFED  122 (175)
T ss_dssp             CCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSSC--STTGGGGEEEEESCCSSCCHHHHHHHCTT
T ss_pred             EEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCccc--cccccCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            5677899999999999999999999997 55688999999998876543  34456789999999999999999999999


Q ss_pred             cCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           80 FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        80 ~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      |++|..+     ..++++++||||+|+++++|++||+.||+..|.+++|+|++|.++
T Consensus       123 ~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          123 ALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             cCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9987655     467889999999999999999999999999999999999999875

>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=99.91  E-value=2.5e-24  Score=179.05  Aligned_cols=129  Identities=23%  Similarity=0.425  Sum_probs=108.3

Q ss_pred             CCCCCC--CcccEEEEEECCHHHHHHHHHccC--ccC---CcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHH
Q 021295            2 KDRKTG--QPRGFGFVTYADPSVVDKVIEDTH--IIN---GKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFK   74 (314)
Q Consensus         2 ~d~~tg--~~kG~aFV~f~~~~~a~~A~~~~~--~i~---g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~   74 (314)
                      +|+.++  ++++||||+|.++++|++|++.++  .+.   .+.+.+.++.+..   ......++|||.|||+++++++|+
T Consensus        37 ~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~v~nl~~~~t~~~l~  113 (175)
T 3nmr_A           37 RDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEK---NNAVEDRKLFIGMISKKCTENDIR  113 (175)
T ss_dssp             EECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGC---CSCGGGSEEEEESCCTTCCHHHHH
T ss_pred             ecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccc---cccCCCCeEEEcCCCCcCCHHHHH
Confidence            466666  899999999999999999998433  333   4566666554432   234567899999999999999999


Q ss_pred             HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC---CeEEEEeecC
Q 021295           75 DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA---GAQVEVKKAE  134 (314)
Q Consensus        75 ~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~---gr~l~V~~a~  134 (314)
                      ++|++||+|+.|.|++++ ++++++||||+|+++++|++|++.||+..+.   +++|.|++|.
T Consensus       114 ~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          114 VMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999999995 6889999999999999999999999987766   4999999874

>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=99.91  E-value=1.3e-23  Score=188.93  Aligned_cols=136  Identities=15%  Similarity=0.317  Sum_probs=122.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCC-CHHHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSV-NEDEFKDFF   77 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~-~e~~l~~~F   77 (314)
                      |+|+.|++++|||||+|.+.++|++|++  +...+.++.|.|.++.++... ....+.++|||.|||+++ ++++|+++|
T Consensus       128 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~-~~~~~~~~l~v~nlp~~~~~~~~l~~~f  206 (284)
T 3smz_A          128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT-PALLHSRCLCVDRLPPGFNDVDALCRAL  206 (284)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCC-TTTTSCSEEEEECCCTTCCCHHHHHHHT
T ss_pred             EeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCC-cccCCccEEEEecCCcccCCHHHHHHHh
Confidence            3577899999999999999999999996  556889999999998776443 344678899999999995 999999999


Q ss_pred             hccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           78 MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        78 ~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      ++||.|+.|.|+++. +++++++|||+|+++++|++|++.||+..|.+++|+|+++.++..
T Consensus       207 ~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          207 SAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             CSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             hCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            999999999999986 789999999999999999999999999999999999999988764

>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=99.90  E-value=2.4e-23  Score=187.87  Aligned_cols=130  Identities=18%  Similarity=0.330  Sum_probs=111.0

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC---CCCCCcceEEEcCCCCC-CCHHHHHHHHhc
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG---SKDFKTKKIFVGGIPSS-VNEDEFKDFFMQ   79 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~---~~~~~~~~l~V~nLp~~-~~e~~l~~~F~~   79 (314)
                      ++++++||||+|.+.++|++|++  +...|.++.|.|+++.+.....   ......++|||.|||++ +++++|+++|++
T Consensus       155 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~  234 (292)
T 2ghp_A          155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG  234 (292)
T ss_dssp             ----CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGG
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhc
Confidence            47899999999999999999998  5568899999999987765443   23456789999999999 999999999999


Q ss_pred             cCCeEEEEEeecCC-CCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           80 FGDVQEHQIMRDHS-TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        80 ~G~v~~v~i~~~~~-~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ||+|+.|+|+++.. |+++++||||+|+++++|++|| .||+..|.+++|.|.+|.++
T Consensus       235 ~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          235 FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             GSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             cCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999999876 5899999999999999999999 99999999999999999876

>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=99.90  E-value=7.6e-23  Score=183.69  Aligned_cols=125  Identities=17%  Similarity=0.291  Sum_probs=108.7

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC---------------------------------
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV---------------------------------   49 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~---------------------------------   49 (314)
                      .|+++||||||+|.+.++|++|++  +...|.++.|.|+++..+...                                 
T Consensus        47 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (282)
T 3pgw_A           47 RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQ  126 (282)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhcc
Confidence            388999999999999999999997  455889999999887554320                                 


Q ss_pred             --------------------------------------------------------------------------CCCCCC
Q 021295           50 --------------------------------------------------------------------------GSKDFK   55 (314)
Q Consensus        50 --------------------------------------------------------------------------~~~~~~   55 (314)
                                                                                                .....+
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  206 (282)
T 3pgw_A          127 GGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPP  206 (282)
T ss_pred             CcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCC
Confidence                                                                                      012234


Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC-CeEEEEeecC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQVEVKKAE  134 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~-gr~l~V~~a~  134 (314)
                      .++|||.|||+++++++|+++|++||.|++|+|+.++     ++||||+|++.++|++||+.||+..|. ++.|+|++++
T Consensus       207 ~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            5789999999999999999999999999999999764     589999999999999999999999999 9999999986

>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=99.89  E-value=6e-23  Score=167.66  Aligned_cols=126  Identities=18%  Similarity=0.298  Sum_probs=109.2

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHcc---CccCCcEEEEeecCCC------------CCCCCCCCCcceEEEcCCCCCCCH
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIEDT---HIINGKQVEIKRTIPK------------GAVGSKDFKTKKIFVGGIPSSVNE   70 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~~---~~i~g~~i~v~~~~~~------------~~~~~~~~~~~~l~V~nLp~~~~e   70 (314)
                      ....+|+++|+|.+.++|++|++++   ..+++ .+.++++..+            ........+.++|||+|||+++++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~   87 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK   87 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSC
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCH
Confidence            4578999999999999999999743   47888 8888876542            122334567789999999999999


Q ss_pred             HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           71 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        71 ~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      ++|+++|++||+|++|+|+++     +++||||+|+++++|++||+.||+..|.+++|+|+++.+++
T Consensus        88 ~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           88 TELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999999999999999999876     58899999999999999999999999999999999998764

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

Probab=99.88  E-value=2.4e-23  Score=167.21  Aligned_cols=125  Identities=19%  Similarity=0.285  Sum_probs=85.7

Q ss_pred             EEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeec
Q 021295           12 FGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRD   91 (314)
Q Consensus        12 ~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~   91 (314)
                      ++|++++|...+..||+.   +.+....-.........+.+..+.++|||.|||+++++++|+++|++||+|+.|+|+.+
T Consensus         6 ~~~~~~~~~~~~~~a~~~---~~g~~~~g~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~   82 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMAS---MTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD   82 (135)
T ss_dssp             --------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCC
T ss_pred             cccccccCCCchhhhhhh---ccCCCCCCCCCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec
Confidence            344455555555556554   33322222222223333445567789999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295           92 HSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        92 ~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      +.++++++||||+|+++++|++||+.||+..|.+++|+|+++++..+.
T Consensus        83 ~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           83 RYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             SSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             CCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            999999999999999999999999999999999999999999886554

>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=99.88  E-value=2.2e-22  Score=172.88  Aligned_cols=123  Identities=15%  Similarity=0.257  Sum_probs=102.7

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC---------------------------------CC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS---------------------------------KD   53 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~---------------------------------~~   53 (314)
                      +||||||+|++.++|++||+  +...+.++.|.|.++..+...+.                                 ..
T Consensus        41 ~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~  120 (205)
T 3tyt_A           41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ  120 (205)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccC
Confidence            58999999999999999998  55689999999998753211000                                 01


Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCe--EEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe----E
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDV--QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA----Q  127 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v--~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr----~  127 (314)
                      .+.++|||.|||++++|++|+++|++||.|  ++|+|+.++  ++.+++|||+|++.++|++||+.||+.+|.++    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            345689999999999999999999999999  899998875  45679999999999999999999999999886    5


Q ss_pred             EEEeec
Q 021295          128 VEVKKA  133 (314)
Q Consensus       128 l~V~~a  133 (314)
                      +.|++|
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777665

>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=99.88  E-value=3.6e-22  Score=164.12  Aligned_cols=87  Identities=16%  Similarity=0.248  Sum_probs=82.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||++++|++|+++|++||+|+.|+|+.++.++++++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      +|++...
T Consensus       115 ~a~~~~~  121 (156)
T 1h2v_Z          115 WDAGFKE  121 (156)
T ss_dssp             EESCCCT
T ss_pred             ECCCCCC
Confidence            9987543

>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=99.88  E-value=3e-22  Score=152.09  Aligned_cols=83  Identities=25%  Similarity=0.560  Sum_probs=79.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||+|||+++||++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+..|.+++|+|++
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            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 021295          133 AEP  135 (314)
Q Consensus       133 a~~  135 (314)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>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=99.88  E-value=7.2e-22  Score=172.37  Aligned_cols=122  Identities=17%  Similarity=0.270  Sum_probs=105.5

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC-------------------------------CCCCc
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS-------------------------------KDFKT   56 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~-------------------------------~~~~~   56 (314)
                      ++||||+|.+.++|++|++  +...|.++.|.|+++.+......                               ...+.
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS  151 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCC
Confidence            8999999999999999997  55688999999988765421110                               12346


Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC-CeEEEEeecC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQVEVKKAE  134 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~-gr~l~V~~a~  134 (314)
                      ++|||.|||+++++++|+++|++|| +|+.|+|+.+     .++||||+|++.++|++||+.||+..|. +++|+|++++
T Consensus       152 ~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~  226 (229)
T 2adc_A          152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  226 (229)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEec
Confidence            8999999999999999999999999 9999999764     3689999999999999999999999999 9999999998


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      ++
T Consensus       227 ~~  228 (229)
T 2adc_A          227 ST  228 (229)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.88  E-value=1.2e-21  Score=176.05  Aligned_cols=122  Identities=15%  Similarity=0.308  Sum_probs=112.7

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeE
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ   84 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~   84 (314)
                      ++++|||||+|.++++|++|++  +...+.++.|.|.++.          ...+|||.|||+++++++|+++|++||+|+
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~  123 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP----------TDALLCVANLPPSLTQQQFEELVRPFGSLE  123 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----------CSCEEEEESCCTTCCHHHHHHHHGGGSCEE
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC----------CCCEEEEcCCCCcCCHHHHHHHHHhcCCee
Confidence            5789999999999999999997  5558899999998743          347999999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           85 EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        85 ~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      .|.|+.++.++++++||||+|+++++|++|++.|++..|.+++|.|.++.+...
T Consensus       124 ~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          124 RCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             EEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            999999999999999999999999999999999999999999999999987654

>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=99.87  E-value=9.5e-22  Score=174.99  Aligned_cols=121  Identities=21%  Similarity=0.383  Sum_probs=108.5

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeE
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ   84 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~   84 (314)
                      .++|+||||+|.+.++|++|++  +...|.++.|.|+++.+          .++|||.|||+++|+++|+++|++||+|+
T Consensus        55 ~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~----------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~  124 (261)
T 3sde_A           55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH----------GAALTVKNLSPVVSNELLEQAFSQFGPVE  124 (261)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC----------SSEEEEESCCTTCCHHHHHHHHGGGSCEE
T ss_pred             eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc----------CCcccccCCCCCCCHHHHHHHHHhcCCeE
Confidence            4679999999999999999998  55688999999998753          57899999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc-CCeeeC---CeEEEEeecCCCCC
Q 021295           85 EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELA---GAQVEVKKAEPKKP  138 (314)
Q Consensus        85 ~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l-~~~~~~---gr~l~V~~a~~~~~  138 (314)
                      .|.|+.+ .++++++||||+|++.++|++||+.| +...+.   +++|.|+++.+...
T Consensus       125 ~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          125 KAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             EEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             EEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence            9999999 68999999999999999999999999 455554   89999999887644

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.87  E-value=7.6e-22  Score=167.93  Aligned_cols=122  Identities=17%  Similarity=0.272  Sum_probs=105.4

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC-------------------------------CCCCCc
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG-------------------------------SKDFKT   56 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~-------------------------------~~~~~~   56 (314)
                      ++||||+|.++++|++|++  +...+.++.|.|.++.+.....                               ....+.
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  120 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS  120 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCc
Confidence            8999999999999999998  5568899999998876442110                               012347


Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC-CeEEEEeecC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQVEVKKAE  134 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~-gr~l~V~~a~  134 (314)
                      ++|||.|||+++++++|+++|++|| +|+.|+|+++     .+++|||+|+++++|++|++.||+..|. +++|+|.+++
T Consensus       121 ~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~  195 (198)
T 1qm9_A          121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  195 (198)
T ss_dssp             CEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeec
Confidence            8999999999999999999999999 9999999765     2789999999999999999999999999 9999999988


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      ++
T Consensus       196 ~~  197 (198)
T 1qm9_A          196 ST  197 (198)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=1.2e-20  Score=146.96  Aligned_cols=90  Identities=22%  Similarity=0.484  Sum_probs=84.3

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .+..+.++|||.|||+++++++|+++|++||+|+.|+|++++.++++++||||+|+++++|++||+.||+..|.++.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35567899999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      +++.++....
T Consensus        90 ~~a~~~~~~~   99 (115)
T 2dgo_A           90 NWATRKPPAP   99 (115)
T ss_dssp             EESSCCCCCS
T ss_pred             EEccCCCCCC
Confidence            9999876543

>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=99.86  E-value=3.7e-21  Score=149.89  Aligned_cols=91  Identities=19%  Similarity=0.428  Sum_probs=84.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCCCC
Q 021295          131 KKAEPKKPNLP  141 (314)
Q Consensus       131 ~~a~~~~~~~~  141 (314)
                      +++.++....+
T Consensus       100 ~~a~~~~~~~~  110 (115)
T 2cpz_A          100 QLKRSKNDSKS  110 (115)
T ss_dssp             ECCCCSCCCCC
T ss_pred             EEcCCCCcCCC
Confidence            99998765443

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

Probab=99.86  E-value=2.8e-21  Score=149.56  Aligned_cols=84  Identities=15%  Similarity=0.285  Sum_probs=80.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||++++|++|+++|++||+|++|+|++|+.|++++|||||+|++.++|++||+.||+..|.+++|+|++|
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            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 021295          134 EPKK  137 (314)
Q Consensus       134 ~~~~  137 (314)
                      ...+
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7654

>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=99.86  E-value=3e-21  Score=174.11  Aligned_cols=118  Identities=14%  Similarity=0.236  Sum_probs=102.2

Q ss_pred             cccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccC-CeEEE
Q 021295            9 PRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFG-DVQEH   86 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G-~v~~v   86 (314)
                      +++||||+|.++++|++|++ +...+.++.|.|.++           +.++|||.|||+++++++|+++|++|| +|+.|
T Consensus        80 ~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~-----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v  148 (292)
T 2ghp_A           80 NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL-----------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSI  148 (292)
T ss_dssp             SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC-----------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEE
T ss_pred             CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC-----------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEE
Confidence            58999999999999999997 556889999999875           368999999999999999999999999 99999


Q ss_pred             EEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           87 QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        87 ~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      .|+.++. +++++||||+|.++++|++|++.||+..|.+++|.|.++.+...
T Consensus       149 ~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          149 RLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             ECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             EEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            9998865 77899999999999999999999999999999999999887654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=1e-21  Score=146.75  Aligned_cols=83  Identities=24%  Similarity=0.534  Sum_probs=77.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc-CCeeeCCeEEEEeec
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQVEVKKA  133 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l-~~~~~~gr~l~V~~a  133 (314)
                      +++|||+|||+++||++|+++|++|| +|++|+|++|+.|+++|+||||+|+++++|++||+.+ +.+.|.+++|.|++|
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            47899999999999999999999999 8999999999999999999999999999999999987 567899999999999


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      .+++.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.85  E-value=1e-20  Score=143.30  Aligned_cols=88  Identities=20%  Similarity=0.351  Sum_probs=83.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|++|+|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.+++..
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99987654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=7.5e-21  Score=145.14  Aligned_cols=90  Identities=20%  Similarity=0.380  Sum_probs=84.1

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .+..+.++|||.|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      +++.++....
T Consensus        90 ~~a~~~~~~~   99 (103)
T 2cq0_A           90 EWAKPSTNSG   99 (103)
T ss_dssp             EESSCCCCSC
T ss_pred             EECCCCCCCC
Confidence            9999876543

>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=8.5e-21  Score=143.75  Aligned_cols=89  Identities=44%  Similarity=0.765  Sum_probs=82.8

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++||+ ||...|.+++|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            345678999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      +++.++....
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2dgs_A           84 KRAEPRDSKS   93 (99)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCcccC
Confidence            9999876543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.7e-20  Score=145.21  Aligned_cols=89  Identities=30%  Similarity=0.561  Sum_probs=82.3

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ..++.+.++|||.|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.|+. .|.+++|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999999999998 89999999


Q ss_pred             EeecCCCCCC
Q 021295          130 VKKAEPKKPN  139 (314)
Q Consensus       130 V~~a~~~~~~  139 (314)
                      |+++.+....
T Consensus        90 V~~a~~~~~~   99 (116)
T 2cqd_A           90 VNLAYLGAKP   99 (116)
T ss_dssp             EEESTTTCCC
T ss_pred             EEEcccCCCc
Confidence            9999876433

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=6.2e-21  Score=145.57  Aligned_cols=89  Identities=24%  Similarity=0.367  Sum_probs=83.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+
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            45567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      ++.+..+..
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dnm_A           89 VARYGRRDL   97 (103)
T ss_dssp             ECSSCCSCC
T ss_pred             ECCcCCCCC
Confidence            999876543

>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=99.85  E-value=5.2e-21  Score=158.71  Aligned_cols=126  Identities=17%  Similarity=0.245  Sum_probs=81.4

Q ss_pred             EEECCHHHHHHHHHccCc----cCCcEEEEeecCC----------------CCCCCCCCCCcceEEEcCCCCCCCHHHHH
Q 021295           15 VTYADPSVVDKVIEDTHI----INGKQVEIKRTIP----------------KGAVGSKDFKTKKIFVGGIPSSVNEDEFK   74 (314)
Q Consensus        15 V~f~~~~~a~~A~~~~~~----i~g~~i~v~~~~~----------------~~~~~~~~~~~~~l~V~nLp~~~~e~~l~   74 (314)
                      ++|++.++|+.|+..+..    ..++.+...+...                ....+....+.++|||.|||+++++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            788889998888874321    1122222221100                11112234556789999999999999999


Q ss_pred             HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCCC
Q 021295           75 DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  140 (314)
Q Consensus        75 ~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~~  140 (314)
                      ++|++||+|+.|.|+.++.++++++||||+|++.++|++||+.||++.|.+++|.|.++.++.+..
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            999999999999999999999999999999999999999999999999999999999998776543

>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=99.85  E-value=1.7e-20  Score=144.97  Aligned_cols=90  Identities=26%  Similarity=0.417  Sum_probs=83.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC------CeeeC
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN------KLELA  124 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~------~~~~~  124 (314)
                      ....+.++|||.|||+++++++|+++|++||+|+.|+|++++.++++++||||+|++.++|++||+.||      .+.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            345678899999999999999999999999999999999999999999999999999999999999999      99999


Q ss_pred             CeEEEEeecCCCCCCC
Q 021295          125 GAQVEVKKAEPKKPNL  140 (314)
Q Consensus       125 gr~l~V~~a~~~~~~~  140 (314)
                      +++|+|+++.++....
T Consensus        90 g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SCEEEEECCCCCCCCC
T ss_pred             CEEEEEEECCCCccCC
Confidence            9999999999876543

>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=99.84  E-value=1.2e-20  Score=144.46  Aligned_cols=89  Identities=27%  Similarity=0.506  Sum_probs=83.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .+..+.++|||.|||+++++++|+++|++||+|++|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 021295          131 KKAEPKKPN  139 (314)
Q Consensus       131 ~~a~~~~~~  139 (314)
                      +++.+++..
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999887654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=7.7e-21  Score=144.74  Aligned_cols=89  Identities=27%  Similarity=0.517  Sum_probs=83.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      ++.++....
T Consensus        88 ~a~~~~~~~   96 (102)
T 2cqb_A           88 LAKPMRIKE   96 (102)
T ss_dssp             ECCCCCCCC
T ss_pred             eCCCCCCCC
Confidence            999876554

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.2e-20  Score=141.67  Aligned_cols=86  Identities=29%  Similarity=0.559  Sum_probs=81.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .++++|||.|||+++++++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|+++
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            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 021295          134 EPKKPN  139 (314)
Q Consensus       134 ~~~~~~  139 (314)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

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

Probab=99.84  E-value=2.3e-20  Score=141.63  Aligned_cols=87  Identities=15%  Similarity=0.458  Sum_probs=81.5

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|++|+|+.++ ++++++||||+|+++++|++||+.||+..|.+++|+|
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 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            355678999999999999999999999999999999999997 8999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      +++.++..
T Consensus        91 ~~a~~~~~   98 (100)
T 2do4_A           91 AISNSGPS   98 (100)
T ss_dssp             EECCCCSC
T ss_pred             EECCCCCC
Confidence            99987643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.8e-20  Score=143.92  Aligned_cols=91  Identities=26%  Similarity=0.445  Sum_probs=84.2

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeec-CCCCCcceEEEEEeCChHHHHHHHHhc-CCeeeCCeE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRD-HSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQ  127 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~-~~~g~~rG~afV~F~~~~~a~~a~~~l-~~~~~~gr~  127 (314)
                      ...+.+.++|||.|||+++++++|+++|++||+|+.|+|+++ +.++++++||||+|+++++|++||+.| |...|.+++
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            345667899999999999999999999999999999999999 789999999999999999999999999 999999999


Q ss_pred             EEEeecCCCCCCC
Q 021295          128 VEVKKAEPKKPNL  140 (314)
Q Consensus       128 l~V~~a~~~~~~~  140 (314)
                      |+|+++.++....
T Consensus        89 l~v~~a~~~~~~~  101 (107)
T 2cph_A           89 LVLEWADSEVTVQ  101 (107)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999999876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.7e-20  Score=139.66  Aligned_cols=85  Identities=22%  Similarity=0.443  Sum_probs=80.7

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCC
Q 021295          131 KKAEP  135 (314)
Q Consensus       131 ~~a~~  135 (314)
                      +++++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99874

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=9.2e-21  Score=144.31  Aligned_cols=88  Identities=32%  Similarity=0.590  Sum_probs=82.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99887654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.1e-20  Score=143.15  Aligned_cols=89  Identities=33%  Similarity=0.633  Sum_probs=83.1

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ...+.+.++|||.|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++||+. +.+.|.+++|+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   88 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNID   88 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEB
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             EeecCCCCCC
Q 021295          130 VKKAEPKKPN  139 (314)
Q Consensus       130 V~~a~~~~~~  139 (314)
                      |+++.++...
T Consensus        89 V~~a~~~~~~   98 (105)
T 2dh8_A           89 PKPCTPRGMQ   98 (105)
T ss_dssp             CCCSCCSSCC
T ss_pred             EEEccCCCCC
Confidence            9999877654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.6e-20  Score=141.95  Aligned_cols=87  Identities=20%  Similarity=0.374  Sum_probs=80.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCC---CCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS---TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~---~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .+.++|||.|||++++|++|+++|++||+|+.|.|+.++.   |+++++||||+|+++++|++||+.||+..|.+++|+|
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            4578999999999999999999999999999999999876   6689999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      +++.++....
T Consensus        83 ~~a~~~~~~~   92 (98)
T 2cpf_A           83 RISERATKPA   92 (98)
T ss_dssp             ECSSCSSCCC
T ss_pred             EEccCCCCCC
Confidence            9998876543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.84  E-value=4.1e-20  Score=148.72  Aligned_cols=91  Identities=22%  Similarity=0.472  Sum_probs=84.2

Q ss_pred             CCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           49 VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        49 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ...++...++|||+|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|
T Consensus        35 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  114 (139)
T 1u6f_A           35 MNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL  114 (139)
T ss_dssp             SSCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEE
T ss_pred             cCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            33456678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecCCCCCC
Q 021295          129 EVKKAEPKKPN  139 (314)
Q Consensus       129 ~V~~a~~~~~~  139 (314)
                      +|++++++...
T Consensus       115 ~v~~a~~~~~~  125 (139)
T 1u6f_A          115 KVALAASGHQR  125 (139)
T ss_dssp             EEEESSCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99999876543

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

Probab=99.84  E-value=4.2e-21  Score=144.51  Aligned_cols=84  Identities=19%  Similarity=0.381  Sum_probs=77.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCC--eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCe----eeCC
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD--VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL----ELAG  125 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~--v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~----~~~g  125 (314)
                      .+....+|||+|||+++||++|+++|++||.  |++|+|++|+.|+++||||||+|+++++|++||+.||+.    .|++
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3456789999999999999999999999995  678999999999999999999999999999999999875    5999


Q ss_pred             eEEEEeecCC
Q 021295          126 AQVEVKKAEP  135 (314)
Q Consensus       126 r~l~V~~a~~  135 (314)
                      ++|.|++|++
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999975

>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=99.84  E-value=2.3e-20  Score=136.55  Aligned_cols=82  Identities=23%  Similarity=0.494  Sum_probs=78.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      +.+|||+|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++|++.||+..|.+++|+|+++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 021295          136 KK  137 (314)
Q Consensus       136 ~~  137 (314)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.2e-20  Score=142.56  Aligned_cols=89  Identities=19%  Similarity=0.442  Sum_probs=82.5

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ..+.+.++|||.|||+++++++|+++|++||+|+.|+|+.+  ++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            45567899999999999999999999999999999999998  8889999999999999999999999999999999999


Q ss_pred             eecCCCCCCCC
Q 021295          131 KKAEPKKPNLP  141 (314)
Q Consensus       131 ~~a~~~~~~~~  141 (314)
                      +++.++....+
T Consensus        88 ~~a~~~~~~~~   98 (103)
T 2d9p_A           88 ALAQRKEERQS   98 (103)
T ss_dssp             EECSSCCCCCC
T ss_pred             EEecccccCCC
Confidence            99998765543

>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=99.84  E-value=1.8e-20  Score=138.35  Aligned_cols=83  Identities=22%  Similarity=0.455  Sum_probs=77.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||+++++++|+++|++||+|++|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+++
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            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>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=99.84  E-value=3.2e-20  Score=142.06  Aligned_cols=88  Identities=20%  Similarity=0.374  Sum_probs=81.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC---eEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG---AQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g---r~l  128 (314)
                      ...+.++|||.|||+++++++|+++|++||+|+.|+|+.++ ++++++||||+|+++++|++||+.||+..|.+   ++|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            44568999999999999999999999999999999999997 78999999999999999999999999999998   999


Q ss_pred             EEeecCCCCCCC
Q 021295          129 EVKKAEPKKPNL  140 (314)
Q Consensus       129 ~V~~a~~~~~~~  140 (314)
                      +|++|.++....
T Consensus        90 ~V~~a~~~~~~~  101 (105)
T 2dnh_A           90 VVKFADTDKESG  101 (105)
T ss_dssp             EEEESCSSCCCS
T ss_pred             EEEECccCcccC
Confidence            999999876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.8e-20  Score=141.01  Aligned_cols=86  Identities=29%  Similarity=0.455  Sum_probs=81.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEE-EEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEH-QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v-~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      .+.++|||.|||+++++++|+++|++||+|++| +|++++.++++++||||+|+++++|++||+.||+..|.+++|+|++
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 9999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 021295          133 AEPKKPN  139 (314)
Q Consensus       133 a~~~~~~  139 (314)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

>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=99.83  E-value=1.6e-20  Score=143.92  Aligned_cols=89  Identities=24%  Similarity=0.472  Sum_probs=82.7

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee---CCeE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL---AGAQ  127 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~---~gr~  127 (314)
                      ..+.+.++|||.|||++++|++|+++|++||+|++|+|+.++.++++++||||+|+++++|++||+.||+..+   .+++
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3556789999999999999999999999999999999999999999999999999999999999999999887   8899


Q ss_pred             EEEeecCCCCCC
Q 021295          128 VEVKKAEPKKPN  139 (314)
Q Consensus       128 l~V~~a~~~~~~  139 (314)
                      |+|+++.++...
T Consensus        88 l~v~~a~~~~~~   99 (106)
T 2dgp_A           88 IQVKPADSESRG   99 (106)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEECCccccc
Confidence            999999887544

>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=99.83  E-value=3.2e-21  Score=143.67  Aligned_cols=84  Identities=17%  Similarity=0.358  Sum_probs=73.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G--~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .+|||+|||++++|++|+++|++||  +|++|+|+.|+.+++++|||||+|++.++|++||+.||+..|.+++|+|+++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 021295          135 PKKPNL  140 (314)
Q Consensus       135 ~~~~~~  140 (314)
                      +..+..
T Consensus        82 ~~~~~~   87 (90)
T 3p5t_L           82 KLEHHH   87 (90)
T ss_dssp             ------
T ss_pred             CCcccc
Confidence            875543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=3.7e-20  Score=138.77  Aligned_cols=84  Identities=23%  Similarity=0.410  Sum_probs=79.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q 021295          131 KKAE  134 (314)
Q Consensus       131 ~~a~  134 (314)
                      ++|+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

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

Probab=99.83  E-value=5.8e-20  Score=140.21  Aligned_cols=86  Identities=20%  Similarity=0.417  Sum_probs=80.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||++++|++|+++|++|+ |++|+|++++.++++++||||+|+++++|++|| .||+..|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            455678999999999999999999999996 999999999999999999999999999999999 899999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            99876544

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.1e-20  Score=144.08  Aligned_cols=89  Identities=25%  Similarity=0.413  Sum_probs=83.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE  122 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~--------~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~  122 (314)
                      .++.+.++|||.|||+++++++|+++|++||+|+        .|+|+.++.++++++||||+|+++++|++||+.||+..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3556789999999999999999999999999999        69999999999999999999999999999999999999


Q ss_pred             eCCeEEEEeecCCCCCC
Q 021295          123 LAGAQVEVKKAEPKKPN  139 (314)
Q Consensus       123 ~~gr~l~V~~a~~~~~~  139 (314)
                      |.+++|+|+++.++...
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999987654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.2e-19  Score=140.87  Aligned_cols=87  Identities=24%  Similarity=0.319  Sum_probs=80.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|++|+|+.++ ++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            44567899999999999999999999999999999999997 58999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++....+.
T Consensus        90 ~a~~~~~~   97 (114)
T 2do0_A           90 MDERALPK   97 (114)
T ss_dssp             ECSCCCCC
T ss_pred             EcccCCCC
Confidence            98865443

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

Probab=99.83  E-value=2.2e-20  Score=143.17  Aligned_cols=87  Identities=18%  Similarity=0.408  Sum_probs=82.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|++|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      +|.++.+
T Consensus        99 ~a~~~~~  105 (106)
T 1p27_B           99 WCFVRGP  105 (106)
T ss_dssp             ESEESSC
T ss_pred             eecCCCC
Confidence            9987643

>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=99.83  E-value=2.5e-20  Score=137.00  Aligned_cols=82  Identities=28%  Similarity=0.549  Sum_probs=78.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||.|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++|++.||+..|.+++|+|++
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            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 021295          133 AE  134 (314)
Q Consensus       133 a~  134 (314)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=1.1e-20  Score=179.77  Aligned_cols=87  Identities=16%  Similarity=0.381  Sum_probs=82.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||++||+++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+.||+++|.+++|+|.
T Consensus        98 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~  177 (437)
T 3pgw_S           98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  177 (437)
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      +|.++..
T Consensus       178 ~a~~~~~  184 (437)
T 3pgw_S          178 VERGRTV  184 (437)
T ss_pred             EeCCCCC
Confidence            9987654

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=9.8e-20  Score=138.87  Aligned_cols=89  Identities=25%  Similarity=0.470  Sum_probs=81.1

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|++|+|+.++.+  +++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC--CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35567899999999999999999999999999999999988643  8999999999999999999999999999999999


Q ss_pred             eecCCCCCCCC
Q 021295          131 KKAEPKKPNLP  141 (314)
Q Consensus       131 ~~a~~~~~~~~  141 (314)
                      +++.++....+
T Consensus        88 ~~a~~~~~~~~   98 (103)
T 2cq3_A           88 NNATARVMTNS   98 (103)
T ss_dssp             EECCSSCCCCC
T ss_pred             EEcccCCCCCC
Confidence            99998765543

>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=99.82  E-value=1.4e-19  Score=137.93  Aligned_cols=87  Identities=21%  Similarity=0.391  Sum_probs=79.5

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ..+.+.++|||.|||+++++++|+++|++||+|+.|+|++++.+  +++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            34567899999999999999999999999999999999998654  6899999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 021295          131 KKAEPKKPN  139 (314)
Q Consensus       131 ~~a~~~~~~  139 (314)
                      +++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            999986543

>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=99.82  E-value=6e-20  Score=140.36  Aligned_cols=86  Identities=23%  Similarity=0.457  Sum_probs=80.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC-CCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~-g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ...+.++|||.|||++++|++|+++|++|| |++|+|++++.+ +++++||||+|+++++|++|| .||+..|.+++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            445679999999999999999999999999 999999999887 899999999999999999999 99999999999999


Q ss_pred             eecCCCCCC
Q 021295          131 KKAEPKKPN  139 (314)
Q Consensus       131 ~~a~~~~~~  139 (314)
                      +++.++...
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999886543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=4.2e-20  Score=139.83  Aligned_cols=86  Identities=20%  Similarity=0.322  Sum_probs=81.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeE-EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE---
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ-EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ---  127 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~-~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~---  127 (314)
                      ...++++|||+|||++++|++|+++|++||+|+ +|+|++++.++++++||||+|+++++|++||+.||+..|.++.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            345689999999999999999999999999999 9999999999999999999999999999999999999999999   


Q ss_pred             -EEEeecCCCC
Q 021295          128 -VEVKKAEPKK  137 (314)
Q Consensus       128 -l~V~~a~~~~  137 (314)
                       |+|++|.+..
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999988754

>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=99.82  E-value=2.3e-20  Score=147.63  Aligned_cols=89  Identities=18%  Similarity=0.396  Sum_probs=83.0

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            34556789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 021295          131 KKAEPKKPN  139 (314)
Q Consensus       131 ~~a~~~~~~  139 (314)
                      ++|.++...
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876543

>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=7.4e-20  Score=142.88  Aligned_cols=85  Identities=31%  Similarity=0.516  Sum_probs=80.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||+|||+++++++|+++|++||+|++|.|+.++ ++++++||||+|++.++|++||+.||+..|.+++|+|++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3567899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      ++++..
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            987654

>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=99.82  E-value=5.3e-20  Score=138.59  Aligned_cols=85  Identities=21%  Similarity=0.388  Sum_probs=80.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ++++|||+|||+++++++|+++|++||+|++|+|+.++.++++++||||+|++.++|++||+.||+..|.++.|+|+++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 021295          135 PKKPN  139 (314)
Q Consensus       135 ~~~~~  139 (314)
                      ++...
T Consensus        81 ~~~~~   85 (96)
T 2x1f_A           81 NSDIS   85 (96)
T ss_dssp             CSSGG
T ss_pred             CCCCC
Confidence            87654

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.82  E-value=3.6e-21  Score=154.84  Aligned_cols=124  Identities=12%  Similarity=0.124  Sum_probs=74.3

Q ss_pred             ccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEe
Q 021295           10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM   89 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~   89 (314)
                      +++||.+|..++.+..++..+..+.+..-.-... ............++|||.|||+++||+||+++|++|+ |++|+|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~-g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~   78 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGS-GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIE   78 (139)
T ss_dssp             ---------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECC
T ss_pred             CCcccccccCccccchhcccchhccCCCCCCCCC-CCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEE
Confidence            4789999999998888877554333222111110 1111122445678999999999999999999999999 7799999


Q ss_pred             ecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           90 RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        90 ~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      +|+. ++++|||||+|+++++|++|| ++|...|.++.|+|..+.+..
T Consensus        79 ~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           79 IGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             CSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             ECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            9975 999999999999999999999 779999999999999887654

>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=99.82  E-value=3.2e-20  Score=147.66  Aligned_cols=88  Identities=24%  Similarity=0.463  Sum_probs=82.7

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      +++.++++
T Consensus       121 ~~a~~~~p  128 (129)
T 2kxn_B          121 DFSITKRP  128 (129)
T ss_dssp             SCCSSSSC
T ss_pred             EEecCCCC
Confidence            99988654

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

Probab=99.82  E-value=3.8e-20  Score=144.30  Aligned_cols=87  Identities=31%  Similarity=0.648  Sum_probs=81.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+.+.++|||.|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+. +...|.+++|+|+
T Consensus        23 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~  101 (116)
T 1x4b_A           23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPK  101 (116)
T ss_dssp             HHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEE
Confidence            344568999999999999999999999999999999999999999999999999999999999999 9999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.++...
T Consensus       102 ~a~~~~~~  109 (116)
T 1x4b_A          102 RAVAREES  109 (116)
T ss_dssp             CCSSCCCC
T ss_pred             ECCCCccC
Confidence            99887543

>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=99.82  E-value=2.4e-19  Score=136.74  Aligned_cols=87  Identities=26%  Similarity=0.504  Sum_probs=80.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||+++++++|+++|++||+|+.|+|+.++.++++++||||+|+++++|++||+.  ...|++++|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCeEEEE
Confidence            3556778999999999999999999999999999999999999999999999999999999999995  67899999999


Q ss_pred             eecCCCCCC
Q 021295          131 KKAEPKKPN  139 (314)
Q Consensus       131 ~~a~~~~~~  139 (314)
                      +++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqg_A           88 KLPNSKQSQ   96 (103)
T ss_dssp             ECCCTTCCC
T ss_pred             EecCCCCcC
Confidence            999987654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.82  E-value=1.4e-20  Score=150.83  Aligned_cols=123  Identities=15%  Similarity=0.151  Sum_probs=79.1

Q ss_pred             ccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCC---eEEE
Q 021295           10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD---VQEH   86 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~---v~~v   86 (314)
                      ++++|.++..++++...+..+....+..-. .  ........+..+.++|||+|||+++||++|+++|++|++   |++|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~-g--~g~~~~~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v   77 (136)
T 2hgl_A            1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQM-G--RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGV   77 (136)
T ss_dssp             -------------------------------------CCSCSSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTE
T ss_pred             CccccccccchHHHHhhccCCCcccCCCCC-C--CCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEE
Confidence            467888888888777666543323222110 0  011112234456789999999999999999999999999   8899


Q ss_pred             EEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           87 QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        87 ~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      +|++|+. ++++|||||+|+++++|++||+ ||...|.++.|+|.++.+++
T Consensus        78 ~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~e  126 (136)
T 2hgl_A           78 HFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTE  126 (136)
T ss_dssp             EEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHHH
T ss_pred             EEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChHH
Confidence            9999987 9999999999999999999999 89999999999999987543

>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=99.82  E-value=5.2e-20  Score=143.51  Aligned_cols=83  Identities=25%  Similarity=0.520  Sum_probs=75.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .+.+|||+|||++++|++|+++|++||+|++|+|++|+.  .+|+||||+|+++++|++||+.||+..|.+++|+|+++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~--~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT--EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC--CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            356899999999999999999999999999999999853  479999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 021295          135 PKKPN  139 (314)
Q Consensus       135 ~~~~~  139 (314)
                      +++..
T Consensus        82 ~~~~~   86 (115)
T 4f25_A           82 SRKER   86 (115)
T ss_dssp             CCCC-
T ss_pred             Ccccc
Confidence            76543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.82  E-value=6.6e-20  Score=138.86  Aligned_cols=85  Identities=21%  Similarity=0.363  Sum_probs=80.2

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCe
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQE--------HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL  121 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~--------v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~  121 (314)
                      .....+.++|||+|||+++++++|+++|++||+|+.        |+|+.++.++++++||||+|+++++|++||+.||+.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            345667899999999999999999999999999999        999999999999999999999999999999999999


Q ss_pred             eeCCeEEEEeecC
Q 021295          122 ELAGAQVEVKKAE  134 (314)
Q Consensus       122 ~~~gr~l~V~~a~  134 (314)
                      .|.+++|+|++|+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999874

>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=99.82  E-value=6.4e-20  Score=141.39  Aligned_cols=88  Identities=30%  Similarity=0.560  Sum_probs=82.5

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      +....+.++|||+|||+++++++|+++|++||+|+.|.|++++.++++++||||+|+++++|++||+.||+..|.+++|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            33556778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      |++++++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99998764

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

Probab=99.82  E-value=9.4e-20  Score=139.18  Aligned_cols=87  Identities=23%  Similarity=0.445  Sum_probs=81.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhc-cCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee-eCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQ-FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE-LAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~-~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~-~~gr~l~  129 (314)
                      +..+.++|||+|||+++++++|+++|++ ||+|++|+|+.++ ++++++||||+|+++++|++||+.||... |.+++|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999998 99999999999999999999999999999 9999999


Q ss_pred             EeecCCCCCC
Q 021295          130 VKKAEPKKPN  139 (314)
Q Consensus       130 V~~a~~~~~~  139 (314)
                      |+++.++...
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999876544

>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=99.82  E-value=7.4e-20  Score=135.59  Aligned_cols=82  Identities=22%  Similarity=0.457  Sum_probs=78.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||.|||+++++++|+++|++||+|++|+|+.++.++++++||||+|+++++|++|+ .||+..|.+++|+|++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4689999999999999999999999999999999999999999999999999999999999 999999999999999998


Q ss_pred             CCC
Q 021295          135 PKK  137 (314)
Q Consensus       135 ~~~  137 (314)
                      +..
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            653

>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=99.82  E-value=5.9e-20  Score=141.79  Aligned_cols=87  Identities=22%  Similarity=0.394  Sum_probs=82.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      ++.++.+
T Consensus       102 ~a~~~~~  108 (110)
T 1oo0_B          102 WCFVKGP  108 (110)
T ss_dssp             ESEESSC
T ss_pred             EcccCCC
Confidence            9987653

>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=99.82  E-value=9.1e-20  Score=136.86  Aligned_cols=84  Identities=24%  Similarity=0.503  Sum_probs=78.1

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ..+.+.++|||.|||+++++++|+++|++||+|++|+|++++. +++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            3456779999999999999999999999999999999999975 889999999999999999999999999999999999


Q ss_pred             eecCC
Q 021295          131 KKAEP  135 (314)
Q Consensus       131 ~~a~~  135 (314)
                      ++++.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            98864

>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=99.82  E-value=1.5e-19  Score=133.41  Aligned_cols=81  Identities=37%  Similarity=0.701  Sum_probs=76.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+.+.++|||+|||++++|++|+++|++||+|+.|+|++++.++++++||||+|+++++|++||+. +...|++++|+|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEE
Confidence            456788999999999999999999999999999999999999999999999999999999999976 7788999999998


Q ss_pred             ec
Q 021295          132 KA  133 (314)
Q Consensus       132 ~a  133 (314)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            76

>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=99.81  E-value=5.8e-20  Score=135.80  Aligned_cols=84  Identities=14%  Similarity=0.401  Sum_probs=78.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCC-cceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR-SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~-~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      .++++|||.|||+++++++|+++|++||+|++|.|+.++.+.. +++||||+|+++++|++|++.||+..|.++.|+|++
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            3568999999999999999999999999999999999987766 899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 021295          133 AEPKK  137 (314)
Q Consensus       133 a~~~~  137 (314)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            97654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.3e-19  Score=133.68  Aligned_cols=83  Identities=20%  Similarity=0.383  Sum_probs=78.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|||.|||+++++++|+++|++| .|++|+|+++ .++++++||||+|+++++|++||+ ||+..|.++.|+|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            44567899999999999999999999999 9999999999 789999999999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 021295          132 KAEPKK  137 (314)
Q Consensus       132 ~a~~~~  137 (314)
                      ++.++.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            998764

>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=99.81  E-value=4.7e-20  Score=139.30  Aligned_cols=85  Identities=15%  Similarity=0.232  Sum_probs=79.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|||.|||++++|++|+++|++|++|+.+.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            45567899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98754

>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=99.81  E-value=1.4e-19  Score=136.39  Aligned_cols=83  Identities=11%  Similarity=0.145  Sum_probs=76.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~----~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ..+.++|||+|||++++|++|+    ++|++||+|++|+|+.++.+   ++||||+|+++++|++||+.||+..|.+++|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3456899999999999999999    99999999999999998766   8899999999999999999999999999999


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      +|++|++...
T Consensus        83 ~V~~a~~~~~   92 (96)
T 2dgx_A           83 LVSLATGASG   92 (96)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEEcCCCCC
Confidence            9999987643

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=1.3e-19  Score=139.95  Aligned_cols=87  Identities=37%  Similarity=0.667  Sum_probs=77.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      +...+.++|||+|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.++ ..|.++.|+|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V   98 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDP   98 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEE
Confidence            345577899999999999999999999999999999999999999999999999999999999999975 9999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      +++.++..
T Consensus        99 ~~a~~~~~  106 (109)
T 2rs2_A           99 KVAFPRRA  106 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987654

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

Probab=99.81  E-value=7.1e-20  Score=143.15  Aligned_cols=83  Identities=20%  Similarity=0.444  Sum_probs=78.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +..+.++|||.|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 021295          132 KAE  134 (314)
Q Consensus       132 ~a~  134 (314)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>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=99.81  E-value=2.3e-19  Score=138.33  Aligned_cols=85  Identities=15%  Similarity=0.438  Sum_probs=77.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||++++|++|+++|++||+|+.|+|+.+   .++++||||+|+++++|++||+.||...|.+++|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34557789999999999999999999999999999999654   457999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      ++++++..
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4a_A           94 EFPRSGRG  101 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EEcccCCC
Confidence            99987654

>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=99.81  E-value=5.5e-21  Score=166.85  Aligned_cols=83  Identities=18%  Similarity=0.374  Sum_probs=78.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G--~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..++|||+|||+++||++|+++|++||  +|++|+|++|+.++++|+||||+|++.++|++||+.||+++|.+++|+|++
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            567899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 021295          133 AEPKK  137 (314)
Q Consensus       133 a~~~~  137 (314)
                      |++..
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            87653

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

Probab=99.81  E-value=8.9e-20  Score=139.09  Aligned_cols=82  Identities=20%  Similarity=0.346  Sum_probs=74.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEEEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVEV  130 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l~V  130 (314)
                      ..+.++|||+|||++++|++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.|+  ..+|.+++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999999975      6899999999999999999775  48899999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      ++|+++....
T Consensus        87 ~~A~~~~~~~   96 (105)
T 1sjq_A           87 QFSNHKELKT   96 (105)
T ss_dssp             CCCSSSSCCC
T ss_pred             EEcCCCCCCc
Confidence            9998876554

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.81  E-value=3.4e-20  Score=147.88  Aligned_cols=90  Identities=20%  Similarity=0.345  Sum_probs=82.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEE--EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCe----eeC
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQE--HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL----ELA  124 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~--v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~----~~~  124 (314)
                      ..+...++|||+|||++++|++|+++|++||+|+.  |+|++|+.++++||||||+|+++ +|++||+.||+.    .|+
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            34567889999999999999999999999999976  99999999999999999999999 999999999999    999


Q ss_pred             CeEEEEeecCCCCCCCC
Q 021295          125 GAQVEVKKAEPKKPNLP  141 (314)
Q Consensus       125 gr~l~V~~a~~~~~~~~  141 (314)
                      +++|+|+++.+++....
T Consensus        97 gr~l~V~~a~~~~~~~~  113 (131)
T 2m2b_A           97 GKTINVEFAKGSKRDMA  113 (131)
T ss_dssp             GCCCCCEECCCSCCCCC
T ss_pred             CEEEEEEECCCCCCCCC
Confidence            99999999988765443

>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=99.81  E-value=4e-20  Score=143.76  Aligned_cols=86  Identities=21%  Similarity=0.436  Sum_probs=80.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ++...++|||.|||+++++++|+++|++||+|+.|+|+.++.++++++||||+|+++++|++|| .||+..|.++.|+|+
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            3445689999999999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (114)
T 2cq4_A          100 ASQAEKN  106 (114)
T ss_dssp             EHHHHHH
T ss_pred             ecCCCcc
Confidence            9987643

>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=99.81  E-value=2e-19  Score=138.02  Aligned_cols=82  Identities=17%  Similarity=0.338  Sum_probs=78.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||++++|++|+++|++||+|++|.|+.++ ++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            44567899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             ecC
Q 021295          132 KAE  134 (314)
Q Consensus       132 ~a~  134 (314)
                      +|.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.6e-19  Score=139.81  Aligned_cols=87  Identities=15%  Similarity=0.283  Sum_probs=79.7

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHH---HHHhccCCeEEEEEeecCCCC---CcceEEEEEeCChHHHHHHHHhcCCeeeC
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFK---DFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLELA  124 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~---~~F~~~G~v~~v~i~~~~~~g---~~rG~afV~F~~~~~a~~a~~~l~~~~~~  124 (314)
                      ....+.++|||.|||++++|++|+   ++|++||+|++|.|++++.++   ++++||||+|+++++|++||+.||+..|+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            345667899999999999999999   999999999999999987654   56699999999999999999999999999


Q ss_pred             CeEEEEeecCCCC
Q 021295          125 GAQVEVKKAEPKK  137 (314)
Q Consensus       125 gr~l~V~~a~~~~  137 (314)
                      +++|+|++|.++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999998875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.80  E-value=4.8e-19  Score=139.71  Aligned_cols=89  Identities=15%  Similarity=0.271  Sum_probs=82.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|+.|+|+.++ ++++++||||+|++.++|++||+.||+..|.+++|+|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             ecCCCCCCCC
Q 021295          132 KAEPKKPNLP  141 (314)
Q Consensus       132 ~a~~~~~~~~  141 (314)
                      +|.+.....+
T Consensus       110 ~a~~~~~~~~  119 (124)
T 2kt5_A          110 LVASQIDLEH  119 (124)
T ss_dssp             EECCTTCCCC
T ss_pred             EeCCCCCCCC
Confidence            9998765544

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

Probab=99.80  E-value=1.3e-19  Score=138.40  Aligned_cols=82  Identities=17%  Similarity=0.363  Sum_probs=77.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+.+.++|||+|||+++|+++|+++|++||+|++|.|++++. ++++|||||+|+++++|++||+ ++++.|.+++|.|+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            456779999999999999999999999999999999999987 9999999999999999999999 79999999999999


Q ss_pred             ecCC
Q 021295          132 KAEP  135 (314)
Q Consensus       132 ~a~~  135 (314)
                      ++.+
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            8765

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.80  E-value=2.6e-20  Score=141.51  Aligned_cols=84  Identities=17%  Similarity=0.256  Sum_probs=79.5

Q ss_pred             CCcceEEEcCCCC------CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC-e
Q 021295           54 FKTKKIFVGGIPS------SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG-A  126 (314)
Q Consensus        54 ~~~~~l~V~nLp~------~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g-r  126 (314)
                      ...++|||.|||+      ++++++|+++|++||+|++|+|++++.|++++|||||+|+++++|++||+.||+..|.+ +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             EEEEeecCCCC
Q 021295          127 QVEVKKAEPKK  137 (314)
Q Consensus       127 ~l~V~~a~~~~  137 (314)
                      +|+|++|.+++
T Consensus        84 ~l~V~~a~~~~   94 (100)
T 3ns6_A           84 RLFLYTMKDVE   94 (100)
T ss_dssp             BCEEEESHHHH
T ss_pred             EEEEEECchhh
Confidence            99999987643

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

Probab=99.80  E-value=2.4e-19  Score=133.73  Aligned_cols=84  Identities=21%  Similarity=0.368  Sum_probs=78.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||.|||+++++++|+++|++||+|+.|+|+++  ++++++||||+|+++++|++||+.||+..|.+++|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456789999999999999999999999999999999984  788999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      +++...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            987654

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.80  E-value=5.3e-20  Score=138.16  Aligned_cols=82  Identities=16%  Similarity=0.266  Sum_probs=76.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ...++|||.|||++++|++|+++|++|++|+.+.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 021295          134 EP  135 (314)
Q Consensus       134 ~~  135 (314)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            63

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4e-19  Score=135.14  Aligned_cols=84  Identities=15%  Similarity=0.272  Sum_probs=75.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc--CCeeeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l--~~~~~~gr~l~  129 (314)
                      ...++++|||+|||++++|++|+++|++||+|++|.|+++      |+||||+|+++++|++||+.|  +.+.|.+++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            4456789999999999999999999999999999998865      789999999999999999976  57889999999


Q ss_pred             EeecCCCCCCCC
Q 021295          130 VKKAEPKKPNLP  141 (314)
Q Consensus       130 V~~a~~~~~~~~  141 (314)
                      |++++++.....
T Consensus        85 V~~a~~~~~~~~   96 (101)
T 2cq1_A           85 IQYSNHKELKTS   96 (101)
T ss_dssp             EEECSCSSCCCC
T ss_pred             EEEcCcccCcCC
Confidence            999998766543

>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=99.80  E-value=7.1e-19  Score=135.42  Aligned_cols=80  Identities=25%  Similarity=0.436  Sum_probs=74.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC-----eE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG-----AQ  127 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g-----r~  127 (314)
                      ....++|||.|||++++|++|+++|++||+|+.|+|+.+       +||||+|+++++|++||+.||+..|.+     ++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            345789999999999999999999999999999999876       799999999999999999999999999     99


Q ss_pred             EEEeecCCCCCC
Q 021295          128 VEVKKAEPKKPN  139 (314)
Q Consensus       128 l~V~~a~~~~~~  139 (314)
                      |+|++|.++...
T Consensus        85 i~V~~a~~~~~~   96 (108)
T 1x4c_A           85 IRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEESSCCSCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999986543

>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=99.80  E-value=6.5e-20  Score=140.00  Aligned_cols=86  Identities=27%  Similarity=0.547  Sum_probs=81.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      +.+.++|||+|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|++.++|++||+.||+..|.+++|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      +.++..
T Consensus        85 a~~~~~   90 (104)
T 1p1t_A           85 AASEKN   90 (104)
T ss_dssp             TTCTTH
T ss_pred             CCCccc
Confidence            987654

>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=99.80  E-value=2.8e-19  Score=137.71  Aligned_cols=87  Identities=23%  Similarity=0.410  Sum_probs=80.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEe-ecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIM-RDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQV  128 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~v~i~-~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l  128 (314)
                      ..+.++|||+|||+++++++|+++|++||+ |++|.|+ .++.++++++||||+|+++++|++||+.|+  .+.|.+++|
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            345789999999999999999999999998 9999999 888889999999999999999999999996  689999999


Q ss_pred             EEeecCCCCCC
Q 021295          129 EVKKAEPKKPN  139 (314)
Q Consensus       129 ~V~~a~~~~~~  139 (314)
                      +|++|.++...
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.80  E-value=1.6e-19  Score=142.41  Aligned_cols=84  Identities=17%  Similarity=0.441  Sum_probs=79.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||+++++++|+++|++||+|++|+|+.++.++++++||||+|+++++|++|| .||+..|.++.|+|+++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            34689999999999999999999999999999999999999999999999999999999999 79999999999999999


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      ++..+
T Consensus       113 ~~~~~  117 (124)
T 2jwn_A          113 RTNMP  117 (124)
T ss_dssp             SCCCS
T ss_pred             CCCCC
Confidence            86544

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

Probab=99.80  E-value=2.1e-19  Score=147.53  Aligned_cols=82  Identities=21%  Similarity=0.387  Sum_probs=77.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G--~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..++|||+|||++++|++|+++|++||  +|++|+|+.|+.+++++|||||+|+++++|++||+.||+..|.+++|+|++
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  999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 021295          133 AEPK  136 (314)
Q Consensus       133 a~~~  136 (314)
                      |.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>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=99.80  E-value=9.6e-19  Score=133.44  Aligned_cols=81  Identities=25%  Similarity=0.454  Sum_probs=74.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|++|+|++        +||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            345678999999999999999999999999999999873        499999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      ++.++....
T Consensus        79 ~a~~~~~~~   87 (103)
T 2dgu_A           79 FAKPPDQKR   87 (103)
T ss_dssp             ECCCCCCCC
T ss_pred             EcCCCcccc
Confidence            998876543

>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=3.2e-19  Score=136.44  Aligned_cols=85  Identities=20%  Similarity=0.321  Sum_probs=78.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~-v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ...+.++|||+|||++++|++|+++|++|+.|++ |.|+.+ .+++++|||||+|+++++|++||+. |...|.++.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999999999999999999999997 889888 7899999999999999999999998 999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      .++.+++.
T Consensus        89 ~~~~~~~~   96 (104)
T 1wg5_A           89 FKSSRAEV   96 (104)
T ss_dssp             EEECTTTS
T ss_pred             EECCHHHH
Confidence            99876654

>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=99.79  E-value=2.6e-19  Score=136.23  Aligned_cols=83  Identities=13%  Similarity=0.131  Sum_probs=73.6

Q ss_pred             CCCCcceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEE
Q 021295           52 KDFKTKKIFVGGIPS-SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~-~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l  128 (314)
                      ...+.++|||+|||+ +++|+||+++|++||+|++|+|+++      ++||||+|+++++|++||+.||  ..+|.+++|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            344678999999999 9999999999999999999999875      4799999999999999999876  467999999


Q ss_pred             EEeecCCCCCCC
Q 021295          129 EVKKAEPKKPNL  140 (314)
Q Consensus       129 ~V~~a~~~~~~~  140 (314)
                      .|.+|..++...
T Consensus        85 ~V~~a~~~~~~~   96 (102)
T 1x4d_A           85 RVHLSQKYKRIK   96 (102)
T ss_dssp             EEEEECCCTTSS
T ss_pred             EEEECCCCCCCC
Confidence            999999765443

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=6.8e-19  Score=133.68  Aligned_cols=84  Identities=18%  Similarity=0.390  Sum_probs=76.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+.+.++|||.|||+++++++|+++|++|++|   +|+.+ .++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45678999999999999999999999999876   56666 688899999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (101)
T 2fc9_A           87 LQGPRGSP   94 (101)
T ss_dssp             ECSSCCCC
T ss_pred             EcCCCCCC
Confidence            99887543

>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=99.79  E-value=2.1e-19  Score=137.05  Aligned_cols=83  Identities=17%  Similarity=0.249  Sum_probs=75.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|||.|||++++|+||+++|++|+.| +|+|++|+ +++++|||||+|+++++|++||+ +|...|.++.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34567899999999999999999999999954 99999997 89999999999999999999995 69999999999999


Q ss_pred             ecCCCC
Q 021295          132 KAEPKK  137 (314)
Q Consensus       132 ~a~~~~  137 (314)
                      .+.+..
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            887654

>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=3.3e-19  Score=139.20  Aligned_cols=83  Identities=19%  Similarity=0.340  Sum_probs=75.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l~  129 (314)
                      ...+.++|||+|||++++|++|+++|++||+|++|.|+++      |+||||+|++.++|++||+.|+  ...|.+++|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            4456789999999999999999999999999999999975      7899999999999999999886  4689999999


Q ss_pred             EeecCCCCCCC
Q 021295          130 VKKAEPKKPNL  140 (314)
Q Consensus       130 V~~a~~~~~~~  140 (314)
                      |++|++++...
T Consensus       101 V~~a~~k~~~~  111 (119)
T 2ad9_A          101 IQFSNHKELKT  111 (119)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEccCCCCCc
Confidence            99999876654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.5e-19  Score=134.41  Aligned_cols=85  Identities=27%  Similarity=0.485  Sum_probs=77.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.|||++++|++|+++|++|   ..|.|+.++.++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            455678999999999999999999999976   47889999889999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      ++++++..
T Consensus        87 ~~a~~~~~   94 (102)
T 2fc8_A           87 DWAKPKGE   94 (102)
T ss_dssp             EECCCCCS
T ss_pred             EEecCCCC
Confidence            99987654

>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=99.79  E-value=1.1e-19  Score=141.47  Aligned_cols=89  Identities=22%  Similarity=0.299  Sum_probs=76.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||.|+.|.+..+..++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            44567899999999999999999999999998544333333377899999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      ++.++....
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpx_A          101 FGKNKKQRS  109 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EccCCCCCC
Confidence            999876544

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

Probab=99.79  E-value=1.4e-19  Score=129.75  Aligned_cols=75  Identities=41%  Similarity=0.729  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +|||+|||+++++++|+++|++||+|++|.|+.++.++++++||||+|+++++|++|++ ||+..|.+++|+|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999999999899999999999999999999998 8999999999999875

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

Probab=99.79  E-value=8.3e-19  Score=130.39  Aligned_cols=79  Identities=25%  Similarity=0.577  Sum_probs=73.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||+|||+++++++|+++|++||+|++|+|+        ++||||+|+++++|++||+.||+..|.+++|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4567899999999999999999999999999999997        56999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 021295          133 AEPKKPN  139 (314)
Q Consensus       133 a~~~~~~  139 (314)
                      +.++...
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9887554

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

Probab=99.79  E-value=1.4e-19  Score=130.35  Aligned_cols=76  Identities=41%  Similarity=0.745  Sum_probs=73.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ++|||+|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++|++.++ ..|++++|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999999999999999999999999999999999 9999999999987

>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=99.79  E-value=2.4e-19  Score=139.49  Aligned_cols=84  Identities=13%  Similarity=0.183  Sum_probs=78.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCe-EEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDV-QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v-~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .+.+.++|||+|||++++|++|+++|++|+.| +.|+|+.|+ ++++++||||+|+++++|++||+. |...|.+++|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            44567899999999999999999999999999 899999998 999999999999999999999998 999999999999


Q ss_pred             eecCCCC
Q 021295          131 KKAEPKK  137 (314)
Q Consensus       131 ~~a~~~~  137 (314)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7e-20  Score=134.65  Aligned_cols=81  Identities=12%  Similarity=0.388  Sum_probs=76.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||.|||+++++++|+++|++||+|+.|.|+.++.++++++||||+|+++++|++||+.||+..|.++.|+|+++
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            46789999999999999999999999999999999999999999999999999999999999999999999998888665


Q ss_pred             C
Q 021295          134 E  134 (314)
Q Consensus       134 ~  134 (314)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=4.5e-19  Score=136.71  Aligned_cols=79  Identities=29%  Similarity=0.483  Sum_probs=73.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +..+|||+|||++++|+||+++|++| .|++|+|+.|+. ++++|||||+|+++++|++|| .+|...|.++.|+|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            45799999999999999999999999 999999999975 999999999999999999999 579999999999999887


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      ++
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            54

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.8e-18  Score=129.12  Aligned_cols=82  Identities=20%  Similarity=0.414  Sum_probs=74.8

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||+|||+++++++|+++|++||+|++|.|+++        ||||+|+++++|++||+.||+..|.+++|+|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            34567899999999999999999999999999999999844        9999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      +++.++....
T Consensus        77 ~~a~~~~~~~   86 (92)
T 2dgt_A           77 QLSTSRLRTA   86 (92)
T ss_dssp             EESSCCCSCC
T ss_pred             EEccCCCCCC
Confidence            9998875543

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

Probab=99.78  E-value=7.3e-19  Score=132.74  Aligned_cols=81  Identities=15%  Similarity=0.226  Sum_probs=72.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCe--eeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL--ELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~--~~~gr~l~  129 (314)
                      ...++++|||+|||++++|++|+++|++||+|++|.|++      .|+||||+|++.++|++|++.|+..  .|.+++|.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            445788999999999999999999999999999999985      3789999999999999999988764  58899999


Q ss_pred             EeecCCCCC
Q 021295          130 VKKAEPKKP  138 (314)
Q Consensus       130 V~~a~~~~~  138 (314)
                      |++++.++.
T Consensus        91 V~~S~~k~l   99 (100)
T 3r27_A           91 VNYSTSQKI   99 (100)
T ss_dssp             EEECSCSCC
T ss_pred             EEecccccc
Confidence            999987653

>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=99.78  E-value=1.5e-18  Score=132.75  Aligned_cols=83  Identities=17%  Similarity=0.221  Sum_probs=73.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l~  129 (314)
                      ...++++|||+|||++++|++|+++|++||+|++|.|+++      |+||||+|+++++|++||+.|+  .+.|.+++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4456789999999999999999999999999999999864      7899999999999999999874  4569999999


Q ss_pred             EeecCCCCCCC
Q 021295          130 VKKAEPKKPNL  140 (314)
Q Consensus       130 V~~a~~~~~~~  140 (314)
                      |++++.+....
T Consensus        85 V~~a~~~~~~~   95 (104)
T 1wex_A           85 FNYSTSKRITR   95 (104)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEccCccccC
Confidence            99999876554

>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=99.78  E-value=1.3e-19  Score=137.57  Aligned_cols=85  Identities=22%  Similarity=0.446  Sum_probs=75.7

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecC-CCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~-~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ......++|||+|||+++++++|+++|++|| |++|+|++++ .++++++||||+|++.++|++|| .||+..|.++.|+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            3456789999999999999999999999999 9999999998 68999999999999999999999 8999999999999


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      |+++.++.
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99998754

>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=4.9e-19  Score=129.40  Aligned_cols=74  Identities=11%  Similarity=0.234  Sum_probs=70.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .+..|||+||++.+||++|+++|.+||+|++++|+.      +||||||+|.++++|++|++.||++.+.+++|+|+.|.
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            367899999999999999999999999999999975      58999999999999999999999999999999999985

>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=99.78  E-value=7.8e-20  Score=135.89  Aligned_cols=83  Identities=31%  Similarity=0.627  Sum_probs=74.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|||+|||+++++++|+++|++||+|++|.|++++.++++++||||+|++++ |++|++.||+..|.+++|+|++|.+.
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            58999999999999999999999999999999999999999999999999999 99999999999999999999999887


Q ss_pred             CCCC
Q 021295          137 KPNL  140 (314)
Q Consensus       137 ~~~~  140 (314)
                      ....
T Consensus        81 ~~~~   84 (90)
T 2ki2_A           81 KSLE   84 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            6543

>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=1.2e-18  Score=133.56  Aligned_cols=85  Identities=14%  Similarity=0.258  Sum_probs=77.6

Q ss_pred             CCCCcceEEEcCCCCCC------CHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           52 KDFKTKKIFVGGIPSSV------NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~------~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      .+...++|||+|||+++      ++++|+++|++||+|++|.|+  +.++++++||||+|+++++|++||+.||+..|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34457899999999999      789999999999999999998  4688999999999999999999999999999999


Q ss_pred             e-EEEEeecCCCCC
Q 021295          126 A-QVEVKKAEPKKP  138 (314)
Q Consensus       126 r-~l~V~~a~~~~~  138 (314)
                      + +|+|+++.+.+.
T Consensus        89 ~~~l~V~~a~~~~k  102 (105)
T 2nlw_A           89 QHTFRVNLFTDFDK  102 (105)
T ss_dssp             TCEEEEECSCCCCC
T ss_pred             CceEEEEEcchHhh
Confidence            8 999999987654

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

Probab=99.78  E-value=1.3e-18  Score=139.73  Aligned_cols=82  Identities=28%  Similarity=0.545  Sum_probs=77.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q 021295          132 KA  133 (314)
Q Consensus       132 ~a  133 (314)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>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=99.78  E-value=8.8e-19  Score=136.04  Aligned_cols=84  Identities=21%  Similarity=0.482  Sum_probs=77.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee--------
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL--------  123 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~--------  123 (314)
                      .+.+.++|||.|||+++++++|+++|++||+|+.|+|+.++ ++++++||||+|+++++|++||+.||+..|        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            45567899999999999999999999999999999999998 899999999999999999999999999998        


Q ss_pred             CCeEEEEeecCCC
Q 021295          124 AGAQVEVKKAEPK  136 (314)
Q Consensus       124 ~gr~l~V~~a~~~  136 (314)
                      .+++|.|++|.+.
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999988754

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

Probab=99.78  E-value=6.5e-19  Score=135.90  Aligned_cols=85  Identities=26%  Similarity=0.518  Sum_probs=78.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||+|||+++++++|+++|++||+|++|+|++++.  ++++||||+|++.++|++|++.||+..|.+++|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3556789999999999999999999999999999999998853  48999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 021295          131 KKAEPKK  137 (314)
Q Consensus       131 ~~a~~~~  137 (314)
                      ++++++.
T Consensus       102 ~~a~~~~  108 (109)
T 2err_A          102 NNATARV  108 (109)
T ss_dssp             EECCCSC
T ss_pred             EECCCCc
Confidence            9998763

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=5.8e-19  Score=138.21  Aligned_cols=84  Identities=17%  Similarity=0.267  Sum_probs=77.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD---VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~---v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ...+.++|||+|||+++||++|+++|++|++   |+.|+|+.++. ++++|||||+|+++++|++||+ ||+..|.++.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            3456789999999999999999999999999   89999999976 9999999999999999999999 89999999999


Q ss_pred             EEeecCCCC
Q 021295          129 EVKKAEPKK  137 (314)
Q Consensus       129 ~V~~a~~~~  137 (314)
                      +|.++..++
T Consensus        91 ~V~~a~~~~   99 (118)
T 2db1_A           91 EVFKSHRTE   99 (118)
T ss_dssp             EEEEECHHH
T ss_pred             EEEECCHHH
Confidence            999987654

>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=99.78  E-value=1.5e-18  Score=130.82  Aligned_cols=80  Identities=20%  Similarity=0.368  Sum_probs=73.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC--CeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--GAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~--gr~l~  129 (314)
                      ...++++|||.|||++++|++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||+..|.  +++|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            4456789999999999999999999999999999999854      679999999999999999999999999  99999


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      |++++++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998764

>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=1.4e-18  Score=134.21  Aligned_cols=97  Identities=18%  Similarity=0.454  Sum_probs=79.6

Q ss_pred             CCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHH
Q 021295           34 NGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD  112 (314)
Q Consensus        34 ~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~-~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~  112 (314)
                      .+..|.++.+.+... .......++|||.|||++ +++++|+++|++||+|++|.|        +++||||+|+++++|+
T Consensus         6 ~g~~~~~~~s~~~~~-~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~   76 (110)
T 1wf1_A            6 SGMSLKLQASNVTNK-NDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHAR   76 (110)
T ss_dssp             CSCCCCCCCCCSCCS-CCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHH
T ss_pred             CCcccccccCCCCCC-CCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHH
Confidence            344455554443322 223445689999999999 999999999999999999998        4789999999999999


Q ss_pred             HHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295          113 DLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus       113 ~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      +||+.||+..|++++|+|+++.+.+..
T Consensus        77 ~A~~~l~g~~~~g~~l~V~~a~~~~~~  103 (110)
T 1wf1_A           77 AAVLGENGRVLAGQTLDINMAGEPKPD  103 (110)
T ss_dssp             HHHHHHTTCEETTEECCEEESCCCCSC
T ss_pred             HHHHHcCCCEECCeEEEEEECCCCCCC
Confidence            999999999999999999999865443

>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=99.77  E-value=1.9e-18  Score=133.10  Aligned_cols=83  Identities=19%  Similarity=0.419  Sum_probs=76.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|||+|||+++++++|+++|++||+|+.|+|+++      ++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999976      6899999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      +++++....
T Consensus        95 ~a~~~~~~~  103 (109)
T 1x4g_A           95 WGKESPDMT  103 (109)
T ss_dssp             CCCCCCSSC
T ss_pred             ecCCCCCCC
Confidence            999876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-19  Score=138.00  Aligned_cols=85  Identities=16%  Similarity=0.351  Sum_probs=77.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||+|||+++++++|+++|++|++|+. .++.++.++++++||||+|+++++|++||+ ||+..|.+++|+|+
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            4456789999999999999999999999999988 677777788999999999999999999999 99999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (101)
T 1fj7_A           91 KPKGRDG   97 (101)
T ss_dssp             CCSCCCC
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.77  E-value=1.8e-19  Score=142.32  Aligned_cols=85  Identities=18%  Similarity=0.305  Sum_probs=78.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||+|||++++|++|+++|++||+|+.+.++.+..+++++|||||+|+++++|++||+ ||+..|.++.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            44567899999999999999999999999999987777777899999999999999999999999 89999999999999


Q ss_pred             ecCCCC
Q 021295          132 KAEPKK  137 (314)
Q Consensus       132 ~a~~~~  137 (314)
                      ++.++.
T Consensus       100 ~a~~~~  105 (124)
T 1wel_A          100 PITKKG  105 (124)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            998754

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

Probab=99.77  E-value=2.5e-18  Score=127.82  Aligned_cols=79  Identities=24%  Similarity=0.459  Sum_probs=73.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +..+.++|||+|||+++++++|+++|++||+|++|+|+++        ||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4556789999999999999999999999999999999844        99999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      ++.++..
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9987644

>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=99.77  E-value=1.8e-18  Score=130.93  Aligned_cols=82  Identities=27%  Similarity=0.517  Sum_probs=75.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+.++|||.|||+++++++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            4456789999999999999999999999999999999854      6899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2cpj_A           85 FACHSASL   92 (99)
T ss_dssp             ESSCCSCC
T ss_pred             EcCCCCCC
Confidence            99886544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.6e-18  Score=130.69  Aligned_cols=82  Identities=16%  Similarity=0.293  Sum_probs=74.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +....++|||+|||+++++++|+++|++||+|+ +.|+.+    ++++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            445678999999999999999999999999997 677654    578999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      ++.++++
T Consensus        90 ~a~~~~~   96 (97)
T 2e5j_A           90 LARQQRD   96 (97)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9987653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.76  E-value=1.6e-18  Score=133.99  Aligned_cols=79  Identities=18%  Similarity=0.314  Sum_probs=71.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G-~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ....+|||+|||++++|++|+++|++|| +|+.|+|+.+    +++|||||+|+++++|++||+.||+.+|.+++|+|++
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3467999999999999999999999999 8999998643    4789999999999999999999999999999999999


Q ss_pred             cCCC
Q 021295          133 AEPK  136 (314)
Q Consensus       133 a~~~  136 (314)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8754

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=9.5e-18  Score=126.89  Aligned_cols=80  Identities=21%  Similarity=0.348  Sum_probs=72.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhcc--CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQF--GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~--G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ....+.++|||.|||+++++++|+++|++|  ++|++|.++        ++||||+|+++++|++||+.||+..|.+++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPI   81 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            345567899999999999999999999999  999999875        5699999999999999999999999999999


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      +|++++++..
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpd_A           82 EVTLAKPVDK   91 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987654

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

Probab=99.76  E-value=4.7e-18  Score=127.36  Aligned_cols=82  Identities=22%  Similarity=0.464  Sum_probs=72.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ....++|||+|||++++|++|+++|++||+|++|  +.++.+++   ||||+|+++++|++||+ ||+..|.+++|+|++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456899999999999999999999999999987  56666655   99999999999999999 999999999999998


Q ss_pred             cCCCCCCC
Q 021295          133 AEPKKPNL  140 (314)
Q Consensus       133 a~~~~~~~  140 (314)
                      +.++....
T Consensus        79 a~~~~~~~   86 (94)
T 2e5g_A           79 REQKEFQS   86 (94)
T ss_dssp             SCCSCCCC
T ss_pred             CCcCCCCC
Confidence            87765443

>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=99.76  E-value=1.5e-18  Score=134.01  Aligned_cols=83  Identities=19%  Similarity=0.289  Sum_probs=73.7

Q ss_pred             CCCCcceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEE
Q 021295           52 KDFKTKKIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~-~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l  128 (314)
                      ...+.++|||+|||++ ++|++|+++|++||+|++|+|++      +|+||||+|+++++|++||+.|+  ...|.+++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3456889999999998 99999999999999999999974      37899999999999999999874  567999999


Q ss_pred             EEeecCCCCCCC
Q 021295          129 EVKKAEPKKPNL  140 (314)
Q Consensus       129 ~V~~a~~~~~~~  140 (314)
                      .|.+|..+....
T Consensus        95 ~V~~a~~~~~~~  106 (112)
T 1x4f_A           95 KVDLSEKYKKLV  106 (112)
T ss_dssp             EEEEECSCSSSS
T ss_pred             EEEECccccccc
Confidence            999998776543

>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=2.9e-18  Score=132.05  Aligned_cols=82  Identities=22%  Similarity=0.456  Sum_probs=73.2

Q ss_pred             CCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           49 VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        49 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ....+.+.++|||+|||+++++++|+++|++||+|++|.|+        ++||||+|++.++|++|++.||+..|.+++|
T Consensus        24 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   95 (108)
T 2jvo_A           24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPL   95 (108)
T ss_dssp             ----CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34456778999999999999999999999999999999998        6799999999999999999999999999999


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      +|+++.++..
T Consensus        96 ~V~~a~~~~~  105 (108)
T 2jvo_A           96 EVVYSKLPAK  105 (108)
T ss_dssp             EEESCSCCC-
T ss_pred             EEEEecCCCC
Confidence            9999987643

>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=5.2e-18  Score=124.49  Aligned_cols=77  Identities=29%  Similarity=0.571  Sum_probs=71.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc-CCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l-~~~~~~gr~l~V  130 (314)
                      .+.+.++|||.|||+++++++|+++|++||+|+.|+|+++      ++||||+|+++++|++|++.| ++..|.+++|+|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            4567789999999999999999999999999999999864      789999999999999999998 999999999999


Q ss_pred             eecC
Q 021295          131 KKAE  134 (314)
Q Consensus       131 ~~a~  134 (314)
                      ++|+
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

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

Probab=99.76  E-value=2.1e-18  Score=130.92  Aligned_cols=78  Identities=21%  Similarity=0.436  Sum_probs=73.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|||+|||+++++++|+++|++||+|++|.|+.+     +++||||+|+++++|++|++.||+..|.+++|+|+++.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999987     6889999999999999999999999999999999999987


Q ss_pred             CCC
Q 021295          137 KPN  139 (314)
Q Consensus       137 ~~~  139 (314)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.76  E-value=1.4e-18  Score=132.14  Aligned_cols=85  Identities=28%  Similarity=0.624  Sum_probs=77.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+...++|||+|||+++++++|+++|++||+|+.|+|+.++ ++++++||||+|+++++|++||+  +.+.|+++.|.|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~   81 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLG   81 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEE
Confidence            34467899999999999999999999999999999999998 99999999999999999999999  8899999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.++...
T Consensus        82 ~a~~~~~~   89 (102)
T 2xs2_A           82 PAIRKQNL   89 (102)
T ss_dssp             EEEECC--
T ss_pred             ECCcCcch
Confidence            99876544

>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=99.75  E-value=5.8e-19  Score=126.51  Aligned_cols=75  Identities=35%  Similarity=0.676  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +|||+|||+++++++|+++|++||+|++|.|++++.++++++||||+|+++++|++||+. +...|.+++|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999997 888999999999875

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1e-18  Score=137.58  Aligned_cols=82  Identities=20%  Similarity=0.279  Sum_probs=75.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCe----EEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDV----QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v----~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      .+..+|||+|||+++||+||+++|++|++|    +.|+|+.+ .+++++|||||+|+++++|++||++ |+..|.++.|+
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            346899999999999999999999999875    68999998 5899999999999999999999998 99999999999


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      |..+.+++
T Consensus        99 V~~a~~~e  106 (123)
T 2dha_A           99 LFRSTAAE  106 (123)
T ss_dssp             CEEECHHH
T ss_pred             EEECCHHH
Confidence            99887654

>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=3.3e-18  Score=129.84  Aligned_cols=78  Identities=17%  Similarity=0.364  Sum_probs=72.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ....++|||+|||+++++++|+++|++||+|++|+|+      ++++||||+|++.++|++||+.||+..|.+++|+|++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            3456899999999999999999999999999999998      3578999999999999999999999999999999999


Q ss_pred             cCCC
Q 021295          133 AEPK  136 (314)
Q Consensus       133 a~~~  136 (314)
                      ++++
T Consensus        98 a~~~  101 (101)
T 2la4_A           98 GKER  101 (101)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8864

>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=99.75  E-value=6e-19  Score=135.64  Aligned_cols=84  Identities=19%  Similarity=0.269  Sum_probs=77.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD---VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~---v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      +....++|||+|||++++|++|+++|++|+.   |+.|+|+.++. ++++|||||+|+++++|++||+ +|...|.++.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            4456789999999999999999999999988   89999999987 9999999999999999999999 89999999999


Q ss_pred             EEeecCCCC
Q 021295          129 EVKKAEPKK  137 (314)
Q Consensus       129 ~V~~a~~~~  137 (314)
                      +|.++.+++
T Consensus        85 ~V~~a~~~~   93 (107)
T 2lmi_A           85 EVYEINNED   93 (107)
T ss_dssp             CCEECCHHH
T ss_pred             EEEECCHHH
Confidence            999987654

>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=2.6e-17  Score=124.05  Aligned_cols=82  Identities=18%  Similarity=0.296  Sum_probs=73.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ....+.++|||.||  ++++++|+++|++||+|+.|.|.      ++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34456789999996  89999999999999999999985      46889999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 021295          131 KKAEPKKPNL  140 (314)
Q Consensus       131 ~~a~~~~~~~  140 (314)
                      +++.++....
T Consensus        82 ~~a~~~~~~~   91 (97)
T 1x5p_A           82 NIARKQPMLD   91 (97)
T ss_dssp             ECCSSCCCCC
T ss_pred             EECCCCCCCC
Confidence            9998875543

>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=99.75  E-value=9.8e-18  Score=137.46  Aligned_cols=83  Identities=11%  Similarity=0.153  Sum_probs=74.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEe
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVK  131 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~  131 (314)
                      .+..+|||.||++.++|++|+++|++||+|++|+|+.++    +++||||+|++.++|++|++.||+.+|.+  ++|+|+
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~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            445789999999999999999999999999999997542    58899999999999999999999999966  999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      +++++....
T Consensus       120 ~Ak~~~l~v  128 (164)
T 1sjr_A          120 FSKLTSLNV  128 (164)
T ss_dssp             ECSSSSCCC
T ss_pred             EecCCcccc
Confidence            999876543

>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=99.75  E-value=3.3e-18  Score=127.90  Aligned_cols=80  Identities=18%  Similarity=0.360  Sum_probs=71.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC-eeeCCeEEEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-LELAGAQVEV  130 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~-~~~~gr~l~V  130 (314)
                      ..+.++|||+|||++++|++|+++|++||+ |+.+.|.       +++||||+|+++++|++||+.||+ ..|.+++|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            456789999999999999999999999999 6656553       478999999999999999999999 9999999999


Q ss_pred             eecCCCCCC
Q 021295          131 KKAEPKKPN  139 (314)
Q Consensus       131 ~~a~~~~~~  139 (314)
                      +++.++...
T Consensus        78 ~~a~~~~~~   86 (93)
T 2cqh_A           78 DYSVSKKLR   86 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCcccc
Confidence            999876543

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

Probab=99.60  E-value=8.6e-20  Score=142.34  Aligned_cols=85  Identities=21%  Similarity=0.382  Sum_probs=80.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQE--------HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA  124 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~--------v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~  124 (314)
                      ..+.++|||+|||+++++++|+++|++||+|+.        |.|+.++.++++++||||+|+++++|++||+.||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            456789999999999999999999999999998        999999889999999999999999999999999999999


Q ss_pred             CeEEEEeecCCCC
Q 021295          125 GAQVEVKKAEPKK  137 (314)
Q Consensus       125 gr~l~V~~a~~~~  137 (314)
                      +++|+|+++.++.
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999998764

>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=9.7e-18  Score=126.54  Aligned_cols=78  Identities=22%  Similarity=0.488  Sum_probs=71.4

Q ss_pred             CCCCCcceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           51 SKDFKTKKIFVGGIPS-SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~-~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ....+.++|||+|||+ ++++++|+++|++||+|++|+|.        ++||||+|++.++|++||+.||+..|.+++|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3456789999999998 99999999999999999999983        67999999999999999999999999999999


Q ss_pred             EeecCCC
Q 021295          130 VKKAEPK  136 (314)
Q Consensus       130 V~~a~~~  136 (314)
                      |++++++
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998865

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=4.9e-18  Score=127.62  Aligned_cols=83  Identities=19%  Similarity=0.340  Sum_probs=74.3

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ..+.+.++|||+|||+++++++|+++|++|++|+.|     ..++++++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   85 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345678999999999999999999999999887665     346789999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      +++.++..
T Consensus        86 ~~a~~~~~   93 (96)
T 1fjc_A           86 YYTGEKGG   93 (96)
T ss_dssp             EECSSSCC
T ss_pred             EEcCCCCC
Confidence            99987643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.74  E-value=6.3e-18  Score=133.85  Aligned_cols=83  Identities=12%  Similarity=0.263  Sum_probs=74.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~----~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ..+.++|||+|||+.+++++|+    ++|++||+|++|.|..   +++++|||||+|++.++|++||+.||+..|.+++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4457899999999999999876    6899999999988853   56789999999999999999999999999999999


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      +|++|..+..
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999987654

>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=1.2e-18  Score=137.49  Aligned_cols=83  Identities=18%  Similarity=0.344  Sum_probs=74.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeE--EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ--EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~--~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ...+.++|||+|||+++||++|+++|++| .|+  +|+|+.|+. ++++|||||+|+++++|++||++ ++..|.++.|+
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            34567899999999999999999999999 777  899999976 99999999999999999999997 66999999999


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      |..+.+++
T Consensus       115 V~~a~~~e  122 (126)
T 2hgm_A          115 VFKSSQEE  122 (126)
T ss_dssp             CEEECHHH
T ss_pred             EEECCHHH
Confidence            99887543

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

Probab=99.74  E-value=4.3e-18  Score=142.68  Aligned_cols=85  Identities=15%  Similarity=0.315  Sum_probs=79.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||.|||+++++++|+++|++||+|+.|.|+.++ ++++++||||+|+++++|++||+.||+..|.+++|+|++|
T Consensus        86 ~~~~~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           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456799999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 021295          134 EPKKPN  139 (314)
Q Consensus       134 ~~~~~~  139 (314)
                      ......
T Consensus       165 ~~~~~~  170 (177)
T 2f3j_A          165 ASQIDL  170 (177)
T ss_dssp             SSGGGG
T ss_pred             cCCCCC
Confidence            876443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.74  E-value=1.8e-18  Score=126.01  Aligned_cols=74  Identities=15%  Similarity=0.348  Sum_probs=68.5

Q ss_pred             cceEEEcCCCCCC------CHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe-EE
Q 021295           56 TKKIFVGGIPSSV------NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA-QV  128 (314)
Q Consensus        56 ~~~l~V~nLp~~~------~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr-~l  128 (314)
                      +++|||+|||+++      ++++|+++|++||+|++|.|+  +.++++++||||+|+++++|++||+.||+..|.++ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      779999999999999999988  46889999999999999999999999999999999 88


Q ss_pred             EEe
Q 021295          129 EVK  131 (314)
Q Consensus       129 ~V~  131 (314)
                      +|+
T Consensus        79 ~V~   81 (81)
T 2krb_A           79 RVN   81 (81)
T ss_dssp             CCC
T ss_pred             EeC
Confidence            773

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.74  E-value=1.1e-17  Score=144.23  Aligned_cols=85  Identities=20%  Similarity=0.358  Sum_probs=78.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||+|||+++||++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.+|...+.++.|+|.+
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            34668999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 021295          133 AEPKK  137 (314)
Q Consensus       133 a~~~~  137 (314)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            87654

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

Probab=99.73  E-value=9.5e-18  Score=126.04  Aligned_cols=82  Identities=20%  Similarity=0.319  Sum_probs=74.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEE-EEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEH-QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v-~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .....++|||+|||+++++++|+++|++||+|+.| .|+.++.++    .|||+|+++++|++||+.||+..|.+++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   86 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKV   86 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34457899999999999999999999999999999 488876554    3999999999999999999999999999999


Q ss_pred             eecCCCC
Q 021295          131 KKAEPKK  137 (314)
Q Consensus       131 ~~a~~~~  137 (314)
                      +++.++.
T Consensus        87 ~~a~~~~   93 (96)
T 2e44_A           87 AYIPDEM   93 (96)
T ss_dssp             EECCCCC
T ss_pred             EEcCccc
Confidence            9999873

>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=99.73  E-value=2.4e-17  Score=140.03  Aligned_cols=117  Identities=17%  Similarity=0.314  Sum_probs=91.2

Q ss_pred             CHHHHHHHHHcc--C--ccCCcEEEEeecCCCCCCCC-----CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEe
Q 021295           19 DPSVVDKVIEDT--H--IINGKQVEIKRTIPKGAVGS-----KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM   89 (314)
Q Consensus        19 ~~~~a~~A~~~~--~--~i~g~~i~v~~~~~~~~~~~-----~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~   89 (314)
                      +.+.+.+|+++.  .  ++......+++....+....     .+.+.++|||.|||+++++++|+++|++||+|+.|+|+
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            667788888754  2  33444445555422211111     22356899999999999999999999999999999999


Q ss_pred             ecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           90 RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        90 ~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      ++. +++++|||||+|+++++|++||+.++ ..|.+++|.|.++....
T Consensus       143 ~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          143 RTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDYF  188 (193)
T ss_dssp             ECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC-
T ss_pred             ECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHHH
Confidence            986 58899999999999999999998865 58999999999887653

>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=6.5e-18  Score=131.56  Aligned_cols=76  Identities=24%  Similarity=0.424  Sum_probs=66.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE-----E
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ-----V  128 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~-----l  128 (314)
                      ...++|||.|||++++|++|+++|++||+|+.|.|+.+       +||||+|+++++|++||+.||+.+|++++     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            34689999999999999999999999999999999865       79999999999999999999999999988     6


Q ss_pred             EEeecCCC
Q 021295          129 EVKKAEPK  136 (314)
Q Consensus       129 ~V~~a~~~  136 (314)
                      +|+.+.+.
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            66665543

>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=99.73  E-value=5.6e-18  Score=127.48  Aligned_cols=83  Identities=17%  Similarity=0.387  Sum_probs=75.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~----~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ..+.++|||+|||+++++++|+    ++|++||+|++|.|+.   ++++++||||+|+++++|++|++.||+..|.+++|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999    9999999999999874   45678999999999999999999999999999999


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      +|+++.++..
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999988654

>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=99.72  E-value=1.1e-17  Score=124.24  Aligned_cols=80  Identities=30%  Similarity=0.594  Sum_probs=64.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+..+|||+|||++++|++|+++|++||+|++|+|+++     +||||||+|+++++|+++..  ..+.+.+++|.|+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~--~~~~~~g~~v~v~   79 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG--EDLIIKGISVHIS   79 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT--CEEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC--CCcccCCEEEEEE
Confidence            4567789999999999999999999999999999999875     78999999999999985432  2455679999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      +|.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9987654

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

Probab=99.72  E-value=7.1e-18  Score=126.92  Aligned_cols=79  Identities=22%  Similarity=0.447  Sum_probs=71.3

Q ss_pred             CCCCcceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPS-SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~-~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ...+.++|||+|||+ ++++++|+++|++||+|++|.|.        ++||||+|+++++|++||+.||+..|.+++|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345678999999999 99999999999999999999994        679999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      +++.++..
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99987654

>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=99.72  E-value=1.5e-17  Score=129.22  Aligned_cols=82  Identities=10%  Similarity=0.310  Sum_probs=75.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+.++|||.|||+++++++|+++|++||+|++|.|+.+.   ++++||||+|++.++|++||+.||+..|.++.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3457899999999999999999999999999999999764   4589999999999999999999999999999999999


Q ss_pred             cCCCC
Q 021295          133 AEPKK  137 (314)
Q Consensus       133 a~~~~  137 (314)
                      +.++.
T Consensus        82 a~~~~   86 (115)
T 3lqv_A           82 YNANR   86 (115)
T ss_dssp             CCHHH
T ss_pred             ecCCh
Confidence            98654

>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=99.72  E-value=1.9e-17  Score=127.98  Aligned_cols=82  Identities=15%  Similarity=0.243  Sum_probs=72.3

Q ss_pred             CCCCcceEEE--cCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee-----C
Q 021295           52 KDFKTKKIFV--GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL-----A  124 (314)
Q Consensus        52 ~~~~~~~l~V--~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~-----~  124 (314)
                      ...++++|||  +||+++++|++|+++|++||+|++|.|+.+      |+||||+|+++++|++|++.||+.+|     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3456789999  779999999999999999999999988643      78999999999999999999999988     6


Q ss_pred             CeEEEEeecCCCCCC
Q 021295          125 GAQVEVKKAEPKKPN  139 (314)
Q Consensus       125 gr~l~V~~a~~~~~~  139 (314)
                      +++|.|.++......
T Consensus        95 g~~l~v~~a~~~p~~  109 (114)
T 2cq2_A           95 KITLYLNFVEKVQWS  109 (114)
T ss_dssp             EEECEEEEESCCCCS
T ss_pred             CcEEEEEecccCccc
Confidence            899999999865443

>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=99.72  E-value=2.5e-17  Score=121.88  Aligned_cols=77  Identities=16%  Similarity=0.286  Sum_probs=71.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ..++|||+|||++++|++|+++|++| +|++|+|.      ++++||||+|+++++|++|++.||+..|.+++|+|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46899999999999999999999999 99999884      578999999999999999999999999999999999987


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      ....
T Consensus        77 ~~~~   80 (88)
T 1wg1_A           77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCce
Confidence            6543

>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=99.72  E-value=1.1e-17  Score=129.36  Aligned_cols=78  Identities=10%  Similarity=0.093  Sum_probs=72.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ..++|||.|||+++++++|+++|++||+|++|.|++      +++||||+|++.++|++||+.||+..|.+++|.|++|.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999999874      47899999999999999999999999999999999998


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      ....
T Consensus        83 ~~~~   86 (111)
T 1whx_A           83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            7543

>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=99.71  E-value=4.8e-17  Score=133.61  Aligned_cols=83  Identities=23%  Similarity=0.530  Sum_probs=79.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      .++|||+|||++++|++|+++|++||+|++|.|++++.++++++||||+|+++++|++|++.|++..|.+++|+|.++.+
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            57999999999999999999999999999999999998999999999999999999999999999999999999999887


Q ss_pred             CCC
Q 021295          136 KKP  138 (314)
Q Consensus       136 ~~~  138 (314)
                      ...
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.71  E-value=2.9e-17  Score=128.04  Aligned_cols=79  Identities=13%  Similarity=0.233  Sum_probs=71.7

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCC----hHH----HHHHHH--hcCCee
Q 021295           57 KKIFVGGI----PSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQA----VDDLLA--KGNKLE  122 (314)
Q Consensus        57 ~~l~V~nL----p~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~----~~~----a~~a~~--~l~~~~  122 (314)
                      .+|||+||    |+.++|++|+++|++||+|++|.++.|+.|++++|||||+|.+    +++    |.+|++  .|+++.
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    9999999999999999999999999999999999999999996    333    888888  789999


Q ss_pred             eCCeEEEEeecCC
Q 021295          123 LAGAQVEVKKAEP  135 (314)
Q Consensus       123 ~~gr~l~V~~a~~  135 (314)
                      |++++|+|.....
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999987553

>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=99.71  E-value=4.4e-17  Score=137.70  Aligned_cols=87  Identities=31%  Similarity=0.613  Sum_probs=79.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      .+..+.++|||+|||++++|++|+++|++||+|++|.|++++.++++++||||+|.++++|++||+. +...|.++.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            3455789999999999999999999999999999999999999999999999999999999999988 889999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      .++.++..
T Consensus        87 ~~~~~~~~   94 (196)
T 1l3k_A           87 KRAVSRED   94 (196)
T ss_dssp             EECCC---
T ss_pred             ecccCccc
Confidence            99877643

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.71  E-value=3.9e-17  Score=134.51  Aligned_cols=84  Identities=23%  Similarity=0.425  Sum_probs=79.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|+++++|++|++.|++..|.+++|.|.++.
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            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      +...
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            7654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.71  E-value=1.1e-16  Score=126.58  Aligned_cols=84  Identities=12%  Similarity=0.187  Sum_probs=75.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceE-EEEEeCChHHHHHHHHhcCCeeeCC--eEEEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGF-GFITFDTEQAVDDLLAKGNKLELAG--AQVEV  130 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~-afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V  130 (314)
                      .+...|||.||++.+||++|+++|++||+|++|+|+.+     .++| |||+|+++++|++|++.||+..|.+  ++|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            45568899999999999999999999999999998864     3678 9999999999999999999999988  99999


Q ss_pred             eecCCCCCCCCC
Q 021295          131 KKAEPKKPNLPQ  142 (314)
Q Consensus       131 ~~a~~~~~~~~~  142 (314)
                      ++++++......
T Consensus       101 ~~ak~~~l~v~~  112 (130)
T 3zzy_A          101 DFSKLTSLNVKY  112 (130)
T ss_dssp             EECSCSSCCCCC
T ss_pred             EecCCCceeEEe
Confidence            999988665443

>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=99.71  E-value=1.4e-17  Score=123.13  Aligned_cols=79  Identities=34%  Similarity=0.624  Sum_probs=69.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .++++|||+|||++++|++|+++|++||+|++|+|+.+     +++||||+|+++++|++|+..  .+.+.+++|+|+++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35789999999999999999999999999999999865     689999999999999876443  46679999999999


Q ss_pred             CCCCCC
Q 021295          134 EPKKPN  139 (314)
Q Consensus       134 ~~~~~~  139 (314)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877544

>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=9.5e-18  Score=135.55  Aligned_cols=88  Identities=25%  Similarity=0.384  Sum_probs=74.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEE--E---eecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQ--I---MRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA  126 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~--i---~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr  126 (314)
                      ...++++|||+|||+++++++|+++|++||.|+.+.  +   ++...++++++||||+|.+.++|++||+.||+..|.++
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            345678999999999999999999999999987641  1   11124678999999999999999999999999999999


Q ss_pred             EEEEeecCCCCCC
Q 021295          127 QVEVKKAEPKKPN  139 (314)
Q Consensus       127 ~l~V~~a~~~~~~  139 (314)
                      +|.|.+|.+..+.
T Consensus       121 ~l~V~~a~~~~~~  133 (143)
T 3egn_A          121 PMVVQFARSARPK  133 (143)
T ss_dssp             ECEEEECCCSCC-
T ss_pred             EEEEEECCCCCCc
Confidence            9999999876543

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

Probab=99.70  E-value=5.2e-17  Score=126.18  Aligned_cols=80  Identities=25%  Similarity=0.457  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC---CCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST---SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~---g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ..+++|||+|||++++|++|+++|++||+|+ +.++.++.+   +++++||||+|+++++|++||+.|+  .++++.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4578999999999999999999999999999 888888777   6999999999999999999999983  477887777


Q ss_pred             eecCCC
Q 021295          131 KKAEPK  136 (314)
Q Consensus       131 ~~a~~~  136 (314)
                      ..+.+.
T Consensus        83 ~~~~~~   88 (114)
T 2dnl_A           83 VSSPTI   88 (114)
T ss_dssp             ECCSSS
T ss_pred             ccCCCc
Confidence            655443

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.69  E-value=2.9e-16  Score=123.43  Aligned_cols=80  Identities=16%  Similarity=0.247  Sum_probs=70.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceE-EEEEeCChHHHHHHHHhcCCeeeCC--eEEEEe
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGF-GFITFDTEQAVDDLLAKGNKLELAG--AQVEVK  131 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~-afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~  131 (314)
                      ....|||.||++.+++++|+++|++||+|++|+|+..      .+| |||+|++.++|++|++.||+.+|.+  ++|+|+
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~   97 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIE   97 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEE
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEE
Confidence            3445789999999999999999999999999999752      276 9999999999999999999999987  699999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      +|+++....
T Consensus        98 ~Ak~~~l~v  106 (124)
T 2e5i_A           98 YARPTRLNV  106 (124)
T ss_dssp             CCSCSCCCC
T ss_pred             EecCCccee
Confidence            999886544

>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=99.68  E-value=1.2e-16  Score=117.63  Aligned_cols=72  Identities=24%  Similarity=0.529  Sum_probs=67.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCee
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQF----G-------DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE  122 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~----G-------~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~  122 (314)
                      .+.++|||+|||+++++++|+++|++|    +       +|++|+|+++      ++||||+|+++++|++|+ .||+..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       8999998854      789999999999999999 999999


Q ss_pred             eCCeEEEEee
Q 021295          123 LAGAQVEVKK  132 (314)
Q Consensus       123 ~~gr~l~V~~  132 (314)
                      |.+++|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999974

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

Probab=99.68  E-value=5.3e-17  Score=141.55  Aligned_cols=112  Identities=20%  Similarity=0.299  Sum_probs=80.9

Q ss_pred             HHHHHHH-ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCC---------CHHHHHHHHhccCCeEEEEEeec
Q 021295           22 VVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSV---------NEDEFKDFFMQFGDVQEHQIMRD   91 (314)
Q Consensus        22 ~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~---------~e~~l~~~F~~~G~v~~v~i~~~   91 (314)
                      .+..+|. ...++-++....+...........+.+.++|||+||+.++         +|++|+++|++||+|++|+|+.+
T Consensus        99 ~~~~~~~~~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~  178 (240)
T 3u1l_A           99 IGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES  178 (240)
T ss_dssp             HHHHHHHCSSBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG
T ss_pred             hhhhcccccCcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC
Confidence            3334444 3344555544333322222223345678999999999998         79999999999999999999853


Q ss_pred             CCCCCcceEEEEEeCChHHHHHHHHhcCCeee------------CCeEEEEeecCCCCCC
Q 021295           92 HSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL------------AGAQVEVKKAEPKKPN  139 (314)
Q Consensus        92 ~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~------------~gr~l~V~~a~~~~~~  139 (314)
                            |+||||+|++.++|++|++.|++..|            .++.|.|++|.+...+
T Consensus       179 ------kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          179 ------KNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             ------GTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             ------CCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence                  78999999999999999999999999            8999999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.67  E-value=2.9e-16  Score=128.78  Aligned_cols=81  Identities=19%  Similarity=0.384  Sum_probs=75.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|||.|||+++++++|+++|++||+|++|+|++++ ++++++||||+|+++++|++|++.|++..|.+++|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999996 4679999999999999999999999999999999999999876


Q ss_pred             CC
Q 021295          137 KP  138 (314)
Q Consensus       137 ~~  138 (314)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.66  E-value=1.7e-16  Score=136.07  Aligned_cols=83  Identities=23%  Similarity=0.468  Sum_probs=75.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||.|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|.++.
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            46799999999999999999999999999999999999899999999999999999999999999999999999998876


Q ss_pred             CCC
Q 021295          135 PKK  137 (314)
Q Consensus       135 ~~~  137 (314)
                      ...
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.66  E-value=4e-16  Score=119.32  Aligned_cols=82  Identities=16%  Similarity=0.102  Sum_probs=73.3

Q ss_pred             CCcceEEEcCCCC-----CCCHHHHHHHHhccCCeEEEEEeecCCC-CCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE
Q 021295           54 FKTKKIFVGGIPS-----SVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ  127 (314)
Q Consensus        54 ~~~~~l~V~nLp~-----~~~e~~l~~~F~~~G~v~~v~i~~~~~~-g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~  127 (314)
                      .++++|+|.||..     +.++++|+++|++||+|++|.|++++.+ ++++|||||+|+++++|++|++.||+..|.+++
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4578999999963     2378999999999999999999998654 688999999999999999999999999999999


Q ss_pred             EEEeecCC
Q 021295          128 VEVKKAEP  135 (314)
Q Consensus       128 l~V~~a~~  135 (314)
                      |.|.++.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999875

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.9e-16  Score=115.12  Aligned_cols=77  Identities=10%  Similarity=0.176  Sum_probs=67.9

Q ss_pred             Ccce-EEEcCCCCCCCHHHH----HHHHhcc-CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           55 KTKK-IFVGGIPSSVNEDEF----KDFFMQF-GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        55 ~~~~-l~V~nLp~~~~e~~l----~~~F~~~-G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      +..+ |||.|||+.+++++|    +++|++| |+|.+|       ++   |+|||+|++.++|++|++.|++.+|.+|+|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            4555 999999999999885    5899999 599988       22   899999999999999999999999999999


Q ss_pred             EEeecCCCCCCCC
Q 021295          129 EVKKAEPKKPNLP  141 (314)
Q Consensus       129 ~V~~a~~~~~~~~  141 (314)
                      +|.+|+.+.....
T Consensus        77 ~v~~A~~~sd~~~   89 (96)
T 2diu_A           77 IVSFTPKNRELCE   89 (96)
T ss_dssp             EEESSCCSCCCCC
T ss_pred             EEEecCCCcceeE
Confidence            9999998876543

>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=99.64  E-value=6.4e-16  Score=132.47  Aligned_cols=78  Identities=21%  Similarity=0.336  Sum_probs=72.7

Q ss_pred             CcceEEEcCCC-CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           55 KTKKIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        55 ~~~~l~V~nLp-~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +.++|||+||| +++++++|+++|++||+|++|+|+++     .++||||+|+++++|++||+.||+..|.+++|.|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46899999999 89999999999999999999999876     3789999999999999999999999999999999998


Q ss_pred             CCCC
Q 021295          134 EPKK  137 (314)
Q Consensus       134 ~~~~  137 (314)
                      +.+.
T Consensus        78 ~~~~   81 (205)
T 3tyt_A           78 KQPA   81 (205)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7654

>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=99.63  E-value=5.6e-16  Score=128.29  Aligned_cols=84  Identities=29%  Similarity=0.540  Sum_probs=75.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCC--CcceEEEEEeCChHHHHHHHHhcCCeeeC---CeEEE
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQAVDDLLAKGNKLELA---GAQVE  129 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g--~~rG~afV~F~~~~~a~~a~~~l~~~~~~---gr~l~  129 (314)
                      +.++|||+|||++++|++|+++|++||+|++|+|++++.++  ++++||||+|+++++|++|++.|+...+.   .++|.
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            46899999999999999999999999999999999998886  89999999999999999999999987765   57788


Q ss_pred             EeecCCCCC
Q 021295          130 VKKAEPKKP  138 (314)
Q Consensus       130 V~~a~~~~~  138 (314)
                      +.++.+...
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            887765543

>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=99.63  E-value=6.2e-16  Score=127.23  Aligned_cols=80  Identities=35%  Similarity=0.767  Sum_probs=74.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ++++|||+|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.  ...|.++.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            468999999999999999999999999999999999999999999999999999999999996  468899999998876


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      ++
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            54

>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=99.62  E-value=4.9e-15  Score=114.56  Aligned_cols=84  Identities=10%  Similarity=0.216  Sum_probs=72.4

Q ss_pred             CCCCcceEEEcCCCCCCC-----------HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC
Q 021295           52 KDFKTKKIFVGGIPSSVN-----------EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK  120 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~-----------e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~  120 (314)
                      ...++++|+|.||....+           +++|+++|++||+|++|.| .++   .++|||||+|+++++|++||+.||+
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            455789999999955432           6899999999999999966 554   3799999999999999999999999


Q ss_pred             eeeCCeEEEEeecCCCCCC
Q 021295          121 LELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus       121 ~~~~gr~l~V~~a~~~~~~  139 (314)
                      ..|.+++|+|+++.++...
T Consensus        87 ~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             CEETTEECEEEECCSCCCS
T ss_pred             CEECCcEEEEEEeCCCCCc
Confidence            9999999999999886544

>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=99.61  E-value=3e-15  Score=134.01  Aligned_cols=84  Identities=18%  Similarity=0.392  Sum_probs=76.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ  127 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~----~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~  127 (314)
                      +..++++|||+|||++++|++|+    ++|++||+|++|+|++   ++++++||||+|++.++|++||+.||+..|.+++
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34568999999999999999977    8999999999999886   6778999999999999999999999999999999


Q ss_pred             EEEeecCCCCC
Q 021295          128 VEVKKAEPKKP  138 (314)
Q Consensus       128 l~V~~a~~~~~  138 (314)
                      |+|+++..+..
T Consensus        82 l~v~~a~~~~~   92 (282)
T 3pgw_A           82 MRIQYAKTDSD   92 (282)
T ss_pred             EEEEEeccCcc
Confidence            99999976553

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

Probab=99.59  E-value=3.7e-15  Score=129.69  Aligned_cols=82  Identities=13%  Similarity=0.235  Sum_probs=75.5

Q ss_pred             CCCCcceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIPS-SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~-~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ...+.++|||+|||+ ++++++|+++|++||+|++|+|++++     ++||||+|.++++|++||+.|++..|.+++|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999999874     789999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      .++.++..
T Consensus       105 ~~a~~~~~  112 (229)
T 2adc_A          105 TLSKHQNV  112 (229)
T ss_dssp             ECCSCCCC
T ss_pred             EEecCccc
Confidence            99987643

>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=99.57  E-value=6.1e-15  Score=112.73  Aligned_cols=82  Identities=17%  Similarity=0.220  Sum_probs=71.5

Q ss_pred             CCcceEEEcCC--CCCCC--------HHHHHHHHhccCCeEEEEEeecCCC--CCcceEEEEEeCChHHHHHHHHhcCCe
Q 021295           54 FKTKKIFVGGI--PSSVN--------EDEFKDFFMQFGDVQEHQIMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKL  121 (314)
Q Consensus        54 ~~~~~l~V~nL--p~~~~--------e~~l~~~F~~~G~v~~v~i~~~~~~--g~~rG~afV~F~~~~~a~~a~~~l~~~  121 (314)
                      .+++.|.|.|+  |.++.        ++||+++|++||+|++|.|++++.+  .+++|+|||+|+++++|++|++.||+.
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            35788999997  43443        3799999999999999999988765  468999999999999999999999999


Q ss_pred             eeCCeEEEEeecCC
Q 021295          122 ELAGAQVEVKKAEP  135 (314)
Q Consensus       122 ~~~gr~l~V~~a~~  135 (314)
                      .|.+|+|+|.++..
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            99999999998764

>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=99.56  E-value=9.3e-15  Score=129.68  Aligned_cols=81  Identities=27%  Similarity=0.508  Sum_probs=73.9

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      .....+.++|||+|||+++|+++|+++|++||+|+.|.|.++      ++||||+|.++++|++||+.||+..|.+++|+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            344567789999999999999999999999999999999754      68999999999999999999999999999999


Q ss_pred             EeecCCC
Q 021295          130 VKKAEPK  136 (314)
Q Consensus       130 V~~a~~~  136 (314)
                      |.++.+.
T Consensus        90 v~~a~~~   96 (261)
T 3sde_A           90 IRFATHG   96 (261)
T ss_dssp             EEECCCS
T ss_pred             eeecccC
Confidence            9998764

>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=1.9e-15  Score=125.48  Aligned_cols=85  Identities=16%  Similarity=0.359  Sum_probs=74.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +..+.++|||+|||+++++++|+++|++|+.|.. .++.+..++++++||||+|+++++|++||+ ||+..|.+++|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            4556899999999999999999999999988766 344445678899999999999999999995 89999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      ++.++..
T Consensus        87 ~~~~~~~   93 (175)
T 1fje_B           87 KPKGRDS   93 (175)
T ss_dssp             CCCCSSC
T ss_pred             cCCCccc
Confidence            9987644

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.55  E-value=6.5e-15  Score=124.84  Aligned_cols=80  Identities=14%  Similarity=0.254  Sum_probs=73.9

Q ss_pred             CcceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           55 KTKKIFVGGIPS-SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        55 ~~~~l~V~nLp~-~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ..++|||+|||+ ++++++|+++|++||+|++|+|++++     ++||||+|+++++|++||+.||+..|.+++|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            358999999999 99999999999999999999999874     789999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 021295          134 EPKKPN  139 (314)
Q Consensus       134 ~~~~~~  139 (314)
                      ......
T Consensus        77 ~~~~~~   82 (198)
T 1qm9_A           77 KHQNVQ   82 (198)
T ss_dssp             CCCSCC
T ss_pred             cCCCcC
Confidence            876543

>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=99.54  E-value=1.9e-14  Score=112.17  Aligned_cols=81  Identities=15%  Similarity=0.155  Sum_probs=70.4

Q ss_pred             CcceEEEcCCCC--C---CCHHHHHHHHhccCCeEEEEEeecCC----CCCcceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           55 KTKKIFVGGIPS--S---VNEDEFKDFFMQFGDVQEHQIMRDHS----TSRSRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        55 ~~~~l~V~nLp~--~---~~e~~l~~~F~~~G~v~~v~i~~~~~----~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ++++|+|.|+-.  +   -.++||+++|++||+|++|.|++++.    +.+++|++||+|+++++|++|++.||+.+|.+
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            567888888742  2   23689999999999999999999865    45678999999999999999999999999999


Q ss_pred             eEEEEeecCC
Q 021295          126 AQVEVKKAEP  135 (314)
Q Consensus       126 r~l~V~~a~~  135 (314)
                      |+|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=8.6e-14  Score=105.20  Aligned_cols=67  Identities=13%  Similarity=0.254  Sum_probs=59.0

Q ss_pred             CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCCC
Q 021295           66 SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN  139 (314)
Q Consensus        66 ~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~~  139 (314)
                      .+++|++|+++|++||+|++|.|+.     +++|||||+|+++++|++||+.++.  +.+++|+|+++.++...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            5689999999999999999999983     5799999999999999999998544  67999999998876543

>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=99.51  E-value=5.3e-14  Score=116.15  Aligned_cols=77  Identities=22%  Similarity=0.529  Sum_probs=68.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQF----G-------DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~----G-------~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      +.++|||+|||++++|++|+++|++|    +       .|.++.+.+      +++||||+|+++++|++|+ .||+..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            56899999999999999999999999    6       677777754      3789999999999999999 8999999


Q ss_pred             CCeEEEEeecCCCCC
Q 021295          124 AGAQVEVKKAEPKKP  138 (314)
Q Consensus       124 ~gr~l~V~~a~~~~~  138 (314)
                      .+++|+|.++.+...
T Consensus        76 ~g~~i~v~~~~~~~~   90 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQP   90 (172)
T ss_dssp             TTEECEEECCSSCCC
T ss_pred             cCceeeecCCcccCC
Confidence            999999998876543

>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=99.51  E-value=8.4e-15  Score=111.76  Aligned_cols=72  Identities=17%  Similarity=0.377  Sum_probs=64.3

Q ss_pred             EcCCCCCCCHHHHHHHH------------hccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           61 VGGIPSSVNEDEFKDFF------------MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        61 V~nLp~~~~e~~l~~~F------------~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      +.+||+.+++++|+++|            ++||+|++|.|++++. ++++|||||+|+++++|++|++.||+..|.+++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56788888888777666            9999999999998864 6899999999999999999999999999999999


Q ss_pred             EEeec
Q 021295          129 EVKKA  133 (314)
Q Consensus       129 ~V~~a  133 (314)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99876

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.49  E-value=9.8e-14  Score=117.17  Aligned_cols=77  Identities=22%  Similarity=0.523  Sum_probs=67.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQF----G-------DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~----G-------~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      .+++|||+|||++++|++|+++|++|    +       .|.++.+.      ++++||||+|.++++|++|| .||+..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    5       56666554      35789999999999999999 8999999


Q ss_pred             CCeEEEEeecCCCCC
Q 021295          124 AGAQVEVKKAEPKKP  138 (314)
Q Consensus       124 ~gr~l~V~~a~~~~~  138 (314)
                      .+++|.|.++.+...
T Consensus        76 ~g~~i~v~~~~~~~~   90 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQP   90 (198)
T ss_dssp             TTEEEEEECCCCCCC
T ss_pred             cCceEEEeCCCCCCC
Confidence            999999999887644

>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=99.43  E-value=3.1e-13  Score=123.75  Aligned_cols=80  Identities=14%  Similarity=0.265  Sum_probs=67.2

Q ss_pred             CCCCCCCcceEEEcC--CCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC--
Q 021295           49 VGSKDFKTKKIFVGG--IPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--  124 (314)
Q Consensus        49 ~~~~~~~~~~l~V~n--Lp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~--  124 (314)
                      ....+.++++|||+|  |++.+||++|+++|++||+|++|.|++      .|+||||+|++.++|++||+.||+.++.  
T Consensus        11 v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           11 IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             CCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             ceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            334567789999999  588999999999999999999987753      4789999999999999999999998873  


Q ss_pred             -Ce--EEEEeecC
Q 021295          125 -GA--QVEVKKAE  134 (314)
Q Consensus       125 -gr--~l~V~~a~  134 (314)
                       ++  +|.|.++.
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence             34  56666654

>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=99.40  E-value=1.1e-12  Score=101.47  Aligned_cols=78  Identities=10%  Similarity=0.085  Sum_probs=65.8

Q ss_pred             CCcceEEEcCCCCCCC----------HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           54 FKTKKIFVGGIPSSVN----------EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~----------e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      .+++.|.|.|+-....          ++||+++|++||+|++|.|+++.    ++|++||+|+++++|++|++.||+.+|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4567777777644322          36889999999999999997653    589999999999999999999999999


Q ss_pred             CCeEEEEeecCC
Q 021295          124 AGAQVEVKKAEP  135 (314)
Q Consensus       124 ~gr~l~V~~a~~  135 (314)
                      .+++|.|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=2.6e-11  Score=94.11  Aligned_cols=77  Identities=14%  Similarity=0.190  Sum_probs=67.6

Q ss_pred             CCCCcceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCC-hHHHHHHHHhc--CCeeeCCeE
Q 021295           52 KDFKTKKIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKG--NKLELAGAQ  127 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~-~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~-~~~a~~a~~~l--~~~~~~gr~  127 (314)
                      ...+...|+|.||+++ +++++|+++|++|++|+.|+|+++..      .|||+|++ +++|++|+++|  .++.|++..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            3456789999999999 99999999999999999999998864      59999999 79999999998  478889988


Q ss_pred             EEEeecC
Q 021295          128 VEVKKAE  134 (314)
Q Consensus       128 l~V~~a~  134 (314)
                      ++++...
T Consensus        88 ~~~evL~   94 (121)
T 1owx_A           88 VTWEVLE   94 (121)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            8886544

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=4.7e-11  Score=87.22  Aligned_cols=73  Identities=22%  Similarity=0.307  Sum_probs=61.2

Q ss_pred             CcceEEEcCCCC----CCCH----HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCe
Q 021295           55 KTKKIFVGGIPS----SVNE----DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA  126 (314)
Q Consensus        55 ~~~~l~V~nLp~----~~~e----~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr  126 (314)
                      +.-||+|.-++.    ++-+    .+|.+.|++||+|..|+|+.++        +||+|++.++|.+||+ ||+..+.++
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            445777766652    2223    6788999999999999999874        8999999999999998 899999999


Q ss_pred             EEEEeecCCC
Q 021295          127 QVEVKKAEPK  136 (314)
Q Consensus       127 ~l~V~~a~~~  136 (314)
                      .|+|+.+++.
T Consensus        77 ~LkV~lkt~d   86 (91)
T 2dnr_A           77 TITIALKSPS   86 (91)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998864

>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=99.09  E-value=5.5e-11  Score=92.03  Aligned_cols=66  Identities=14%  Similarity=0.377  Sum_probs=36.5

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC----CCCCcceEEEcCCCCCCCHHH
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS----KDFKTKKIFVGGIPSSVNEDE   72 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~----~~~~~~~l~V~nLp~~~~e~~   72 (314)
                      ..+||||||+|++.++|++||+  +.+.|.++.|.|+++.++.....    ...+.++|||.|||+++|++.
T Consensus        42 ~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           42 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC----------------------------
T ss_pred             CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccccccccccCCCCceEeCCCCCCccccc
Confidence            4589999999999999999997  55689999999999877654332    334456899999999999874

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.04  E-value=4e-10  Score=82.66  Aligned_cols=72  Identities=14%  Similarity=0.221  Sum_probs=61.4

Q ss_pred             CCcceEEEcCCCCC------CCH---HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC
Q 021295           54 FKTKKIFVGGIPSS------VNE---DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA  124 (314)
Q Consensus        54 ~~~~~l~V~nLp~~------~~e---~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~  124 (314)
                      ++.-||+|.-++.+      ..+   .+|.+.|++||+|..|+|+.|+        +||+|.+.++|.+||+ ||+..+.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            45678888888643      232   5688999999999999999884        9999999999999999 8999999


Q ss_pred             CeEEEEeecC
Q 021295          125 GAQVEVKKAE  134 (314)
Q Consensus       125 gr~l~V~~a~  134 (314)
                      +|.|+|++..
T Consensus        84 Gr~L~V~~k~   93 (95)
T 1ufw_A           84 GRAVKISGPS   93 (95)
T ss_dssp             TEEEEEECCC
T ss_pred             CeEEEEeccC
Confidence            9999998754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.03  E-value=1.3e-09  Score=94.05  Aligned_cols=68  Identities=18%  Similarity=0.152  Sum_probs=61.0

Q ss_pred             CCHHHHHHHHhccCCeEEEEEeecC----CCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           68 VNEDEFKDFFMQFGDVQEHQIMRDH----STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        68 ~~e~~l~~~F~~~G~v~~v~i~~~~----~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ..+++|++.|++||+|++|.|+++.    .+.+++|++||+|++.++|++|++.||+.++.+|+|.|.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            3568999999999999999999554    4458999999999999999999999999999999999998753

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.78  E-value=1.1e-08  Score=75.51  Aligned_cols=49  Identities=29%  Similarity=0.550  Sum_probs=42.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc---CccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT---HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~---~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++||||||+|++.++|++||+.+   ..+.+++|.|+++.+++..
T Consensus        35 ~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~~   86 (91)
T 2lxi_A           35 MRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKI   86 (91)
T ss_dssp             SSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCCC
T ss_pred             EecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCCC
Confidence            578999999999999999999999999843   2689999999998876543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.74  E-value=7.7e-08  Score=71.98  Aligned_cols=74  Identities=14%  Similarity=0.141  Sum_probs=67.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhcc-----CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEE
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQF-----GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV  128 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~-----G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l  128 (314)
                      ...++|-|-+||+.++++.|+.+++++     +.|+.|.+..|..      =|+|+|++..+|-+|.-.|++.+|.+++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            346889999999999999999999999     9999999998853      59999999999999999999999999999


Q ss_pred             EEeec
Q 021295          129 EVKKA  133 (314)
Q Consensus       129 ~V~~a  133 (314)
                      +|...
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            98644

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

Probab=98.64  E-value=2e-08  Score=74.81  Aligned_cols=45  Identities=27%  Similarity=0.480  Sum_probs=39.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccC------ccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH------IINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~------~i~g~~i~v~~~~~   45 (314)
                      |+|+.|+++||||||+|.+.++|++|++.++      .|++++|.|+++..
T Consensus        44 ~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           44 IKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             EecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            5789999999999999999999999998332      48899999998754

>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=98.62  E-value=3.1e-08  Score=74.27  Aligned_cols=45  Identities=22%  Similarity=0.578  Sum_probs=40.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      ++|+.|+++||||||+|++.++|++|++  +...|.+++|.|+++.|
T Consensus        52 ~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           52 IRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             EECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             eecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4688999999999999999999999998  55689999999999865

>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=98.59  E-value=6.2e-08  Score=72.84  Aligned_cols=50  Identities=34%  Similarity=0.573  Sum_probs=44.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++||||||+|.+.++|++||++.+.|.++.|.|+++.++....
T Consensus        48 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cqg_A           48 KKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQD   97 (103)
T ss_dssp             EECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCCCC
T ss_pred             EecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCCCCcCC
Confidence            35778999999999999999999999998888999999999998876544

>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=98.56  E-value=2.9e-08  Score=72.94  Aligned_cols=48  Identities=17%  Similarity=0.369  Sum_probs=38.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+.|+++||||||+|++.++|++|++  +...+.++.|.|+++.++..
T Consensus        36 ~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           36 FENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH   85 (90)
T ss_dssp             EECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-----
T ss_pred             EecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCcc
Confidence            4578899999999999999999999997  55689999999999877644

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.54  E-value=1.5e-07  Score=70.10  Aligned_cols=50  Identities=40%  Similarity=0.755  Sum_probs=43.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++|+||||+|++.++|++||+ +.+.|.++.|.|+++.++....
T Consensus        43 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           43 IYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKS   93 (99)
T ss_dssp             CCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECCCCCCCC
T ss_pred             EeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECCCCcccC
Confidence            5678899999999999999999999998 5568999999999998775543

>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=98.52  E-value=2.5e-07  Score=68.85  Aligned_cols=50  Identities=26%  Similarity=0.432  Sum_probs=43.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      ++|+.|+++++||||+|.+.++|++||+  +...|.++.|.|+++.++....
T Consensus        41 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   92 (99)
T 1whw_A           41 PIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS   92 (99)
T ss_dssp             CCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTTC
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcccc
Confidence            4677899999999999999999999997  4458899999999998876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.52  E-value=2e-07  Score=68.94  Aligned_cols=50  Identities=24%  Similarity=0.554  Sum_probs=43.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      ++|+.|+++++||||+|++.++|++|++  +...|.++.|.|+++.++....
T Consensus        39 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   90 (96)
T 1x5t_A           39 MRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG   90 (96)
T ss_dssp             CCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCCC
T ss_pred             EEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCCC
Confidence            4677899999999999999999999999  4458899999999988765443

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

Probab=98.50  E-value=1e-07  Score=72.88  Aligned_cols=46  Identities=11%  Similarity=0.199  Sum_probs=40.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|++.++|++|++  +...|.++.|.|+++...
T Consensus        39 ~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A           39 LLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTT
T ss_pred             EECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            4688999999999999999999999998  555899999999887543

>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=98.50  E-value=3.5e-08  Score=75.82  Aligned_cols=65  Identities=15%  Similarity=0.242  Sum_probs=54.8

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGD   82 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~   82 (314)
                      ++.+++||||+|.+.++|++|++  +...+.++.|.|.++.++...            .+++...++++|+++|++||.
T Consensus        43 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           43 TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             STTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            45679999999999999999998  556899999999998765332            467788899999999999974

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.48  E-value=9.1e-07  Score=65.64  Aligned_cols=75  Identities=28%  Similarity=0.448  Sum_probs=63.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhcc-----CCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQF-----GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~-----G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      ..++|.|.|||.+++++.|+-+|++-     |+|+.|+...        .-|+|+|.++++|+++|++ ..+.|.+.+|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            45799999999999999999999872     6899998865        2699999999999999997 57788899999


Q ss_pred             EeecCCCCC
Q 021295          130 VKKAEPKKP  138 (314)
Q Consensus       130 V~~a~~~~~  138 (314)
                      |....++.+
T Consensus        78 V~P~~~~~~   86 (104)
T 2dhx_A           78 LRPAPPRAP   86 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEcCCCCCc
Confidence            987665543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=1.5e-07  Score=70.61  Aligned_cols=49  Identities=33%  Similarity=0.616  Sum_probs=43.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++|+||||+|++.++|++||+  +.+.|.++.|.|+++.++...
T Consensus        45 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           45 VTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             EECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             EecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            4677899999999999999999999998  556899999999999876543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.47  E-value=2.4e-07  Score=69.37  Aligned_cols=50  Identities=20%  Similarity=0.331  Sum_probs=43.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++++||||+|++.++|++|++  +...|.++.|.|+++.++....
T Consensus        45 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   96 (102)
T 2cqb_A           45 PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE   96 (102)
T ss_dssp             CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             EecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCCC
Confidence            4678899999999999999999999997  5568999999999988765543

>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=98.46  E-value=3.9e-07  Score=69.28  Aligned_cols=50  Identities=12%  Similarity=0.359  Sum_probs=43.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--------cCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--------THIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--------~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++++||||+|.+.++|++||+.        ...|.++.|.|+++.++....
T Consensus        48 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           48 VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             CBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCCC
T ss_pred             EecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccCC
Confidence            46888999999999999999999999983        568999999999988775543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.46  E-value=2.8e-07  Score=70.65  Aligned_cols=50  Identities=24%  Similarity=0.495  Sum_probs=43.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++++||||+|.+.++|++||+  +...|.++.|.|+++.++....
T Consensus        48 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           48 VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCCS
T ss_pred             EEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCCC
Confidence            3577899999999999999999999998  4568999999999988775543

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

Probab=98.45  E-value=2.2e-07  Score=69.81  Aligned_cols=49  Identities=12%  Similarity=0.387  Sum_probs=42.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|++++|||||+|++.++|++||+ +...|.++.|.|+++.++...
T Consensus        47 ~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           47 VRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             EECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECCCCCCC
T ss_pred             eecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEecCCCCC
Confidence            4678899999999999999999999996 445889999999998876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.45  E-value=2.9e-07  Score=67.92  Aligned_cols=49  Identities=24%  Similarity=0.584  Sum_probs=42.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++++||||+|++.++|++|++  +...|.++.|.|+++.++...
T Consensus        38 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           38 MKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             ECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             eecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            3677899999999999999999999998  556899999999998876543

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

Probab=98.45  E-value=1.7e-07  Score=70.17  Aligned_cols=58  Identities=22%  Similarity=0.459  Sum_probs=46.8

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCC------CCCCcceEEEcCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGS------KDFKTKKIFVGGIPS   66 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~------~~~~~~~l~V~nLp~   66 (314)
                      +++||||+|++.++|++|++  +...+.++.|.|+++.++.....      ......+|||++|+.
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~ifvg~L~h  101 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLEH  101 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCSCCCCSCCCSCCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCccccCCCceecCCCCC
Confidence            79999999999999999998  55689999999999877654332      223367899999973

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.44  E-value=1.1e-07  Score=71.57  Aligned_cols=47  Identities=17%  Similarity=0.145  Sum_probs=40.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+ |+++||||||+|+++++|++||+ +.+.|.++.|+|.++.+.+.
T Consensus        47 ~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           47 EIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             EESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCCC
T ss_pred             EECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCCCCC
Confidence            3576 99999999999999999999997 55688999999998776543

>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=98.44  E-value=2.9e-07  Score=69.32  Aligned_cols=49  Identities=31%  Similarity=0.524  Sum_probs=42.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++|+||||+|.+.++|++|++  +...|.++.|.|+++.++...
T Consensus        48 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           48 PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             EecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            4677899999999999999999999999  445899999999998876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.44  E-value=3.9e-07  Score=69.64  Aligned_cols=49  Identities=27%  Similarity=0.514  Sum_probs=43.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++|+||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        56 ~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           56 YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             CBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             EEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCC
Confidence            4677899999999999999999999998  556899999999998876544

>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=98.44  E-value=2.4e-07  Score=66.50  Aligned_cols=46  Identities=24%  Similarity=0.515  Sum_probs=41.0

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+.|+++++||||+|.+.++|++|++  +...+.++.|.|+++.+++
T Consensus        35 ~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           35 WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             ECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             EcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            577899999999999999999999998  5568999999999988763

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.44  E-value=1.4e-07  Score=70.69  Aligned_cols=48  Identities=21%  Similarity=0.496  Sum_probs=41.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+.|+++||||||+|++.++|++||+ +...|.++.|.|+++.++..
T Consensus        49 ~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           49 VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             CCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCSCCCC
T ss_pred             EecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcCCCCC
Confidence            5677899999999999999999999998 44588999999999877644

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.43  E-value=3.4e-07  Score=69.75  Aligned_cols=49  Identities=41%  Similarity=0.711  Sum_probs=42.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc-CccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~-~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++||||||+|.+.++|++||+.+ +.|.++.|.|+++.++...
T Consensus        58 ~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           58 MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             CCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEECCCCCCC
T ss_pred             EECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEccCCCCC
Confidence            467889999999999999999999999843 6889999999998876543

>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=98.43  E-value=2e-07  Score=67.64  Aligned_cols=46  Identities=26%  Similarity=0.558  Sum_probs=39.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      ++|+.|+++++||||+|.+.++|++|++  +...+.++.|.|+++.++
T Consensus        39 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           39 VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            3577899999999999999999999998  456899999999998764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.43  E-value=2.9e-07  Score=68.94  Aligned_cols=49  Identities=27%  Similarity=0.544  Sum_probs=42.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++++||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        45 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           45 VKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             CCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             EeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            4677899999999999999999999997  556899999999998876554

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.42  E-value=3.8e-07  Score=68.62  Aligned_cols=49  Identities=10%  Similarity=0.304  Sum_probs=42.1

Q ss_pred             CCCCCC-CCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKT-GQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~t-g~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.| ++++|||||+|++.++|++||+ +...|.++.|.|+++.++...
T Consensus        47 ~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           47 PREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             CBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCCC
T ss_pred             ecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEccCCCCC
Confidence            467777 9999999999999999999995 445899999999998876554

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

Probab=98.42  E-value=2.2e-07  Score=65.48  Aligned_cols=43  Identities=49%  Similarity=0.758  Sum_probs=37.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|++++|||||+|+++++|++|++ +.+.+.++.|.|+++
T Consensus        32 ~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           32 MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             EecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            4677899999999999999999999998 556889999988764

>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=98.41  E-value=4.4e-07  Score=68.42  Aligned_cols=47  Identities=21%  Similarity=0.364  Sum_probs=40.6

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      +| .|+++||||||+|+++++|++||+ +.+.|.++.|.|.++.+++..
T Consensus        50 ~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~~~~~~~   97 (104)
T 1wg5_A           50 VD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             BC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTTSC
T ss_pred             EC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEECCHHHHH
Confidence            45 799999999999999999999999 556899999999988766543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.41  E-value=3.5e-07  Score=68.68  Aligned_cols=49  Identities=20%  Similarity=0.394  Sum_probs=42.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++++||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        48 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           48 AKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             EECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             eecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            3577899999999999999999999999  445899999999998876543

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.41  E-value=5.7e-07  Score=68.17  Aligned_cols=48  Identities=21%  Similarity=0.309  Sum_probs=42.3

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~   49 (314)
                      +|+.|+++|+||||+|.+.++|++|++.+    ..+.++.|.|+++.++...
T Consensus        44 ~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~~   95 (109)
T 2dis_A           44 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   95 (109)
T ss_dssp             SSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             cCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCCc
Confidence            67889999999999999999999999943    5789999999999877554

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.41  E-value=1.5e-07  Score=70.61  Aligned_cols=46  Identities=20%  Similarity=0.254  Sum_probs=40.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCC-cEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIING-KQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g-~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|.+.++|++|++  +...|.+ +.|.|+++.++
T Consensus        45 ~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           45 PIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             EEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            4688899999999999999999999997  5568888 99999987654

>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=98.40  E-value=3.2e-07  Score=70.34  Aligned_cols=50  Identities=24%  Similarity=0.450  Sum_probs=43.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++|+||||+|.+.++|++||+  +...|.++.|.|+++.++....
T Consensus        58 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~  109 (115)
T 2cpz_A           58 FIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK  109 (115)
T ss_dssp             EECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCCC
T ss_pred             EECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcCC
Confidence            3577899999999999999999999997  5568999999999988765543

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

Probab=98.39  E-value=3.5e-07  Score=70.24  Aligned_cols=50  Identities=38%  Similarity=0.707  Sum_probs=43.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++||||||+|.+.++|++||+ +.+.|.++.|.|+++.++....
T Consensus        60 ~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~~~  110 (116)
T 1x4b_A           60 MRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESG  110 (116)
T ss_dssp             ECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCCCC
T ss_pred             EECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCCCccCC
Confidence            4677899999999999999999999998 4458999999999998875543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.38  E-value=3.3e-07  Score=68.82  Aligned_cols=49  Identities=20%  Similarity=0.374  Sum_probs=42.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++|+||||+|.+.++|++||+  +...|.++.|.|+++.+....
T Consensus        46 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dnm_A           46 PREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD   96 (103)
T ss_dssp             CBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSC
T ss_pred             EeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCC
Confidence            4678899999999999999999999998  556899999999998876443

>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=98.38  E-value=5.1e-07  Score=66.85  Aligned_cols=48  Identities=15%  Similarity=0.339  Sum_probs=42.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      ++|+.|+++++||||+|.+.++|++|++  +...+.++.|.|+++.++..
T Consensus        35 ~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           35 MFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             CBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             EeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            4677899999999999999999999997  55689999999999887644

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.38  E-value=6.6e-07  Score=68.69  Aligned_cols=49  Identities=33%  Similarity=0.650  Sum_probs=41.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc-CccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~-~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++|+||||+|++.++|++||+.+ ..|.++.|.|+++.+....
T Consensus        50 ~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~~   99 (116)
T 2cqd_A           50 ITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKP   99 (116)
T ss_dssp             SCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTTCCC
T ss_pred             EEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEcccCCCc
Confidence            467889999999999999999999999933 3789999999998765433

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.38  E-value=1.6e-07  Score=70.79  Aligned_cols=50  Identities=40%  Similarity=0.812  Sum_probs=43.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|+.|+++|+||||+|++.++|++||+ +.+.|.++.|.|+++.++....
T Consensus        49 ~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a~~~~~~~   99 (105)
T 2dh8_A           49 MKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQP   99 (105)
T ss_dssp             EECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCSCCSSCCT
T ss_pred             eeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEccCCCCCC
Confidence            3577899999999999999999999999 5568999999999988775543

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.36  E-value=3.6e-07  Score=67.88  Aligned_cols=46  Identities=17%  Similarity=0.293  Sum_probs=39.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++|+||||+|.+.++|++||+.  ...|.++.|.|+++..+
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            35678999999999999999999999974  45899999999987643

>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=98.35  E-value=7.8e-07  Score=67.03  Aligned_cols=49  Identities=22%  Similarity=0.335  Sum_probs=41.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--Ccc---CCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HII---NGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i---~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++|+||||+|.+.++|++|++.+  ..+   .++.|.|+++.++...
T Consensus        46 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           46 LKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             CCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             EecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            467889999999999999999999999843  355   7899999998876543

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=98.35  E-value=2.4e-07  Score=65.19  Aligned_cols=43  Identities=35%  Similarity=0.546  Sum_probs=37.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|++++|||||+|+++++|++|++ +.+.+.++.|.|+++
T Consensus        32 ~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           32 PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             EecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            4678899999999999999999999999 556889999888764

>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=98.34  E-value=3.3e-07  Score=66.54  Aligned_cols=43  Identities=35%  Similarity=0.783  Sum_probs=37.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      |+|+.|++++|||||+|.+.++|++|++ +.+.|+++.|.|+++
T Consensus        44 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           44 KMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             EECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             eecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            3577899999999999999999999998 445799999998864

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

Probab=98.34  E-value=3.9e-07  Score=68.69  Aligned_cols=47  Identities=21%  Similarity=0.437  Sum_probs=41.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ++|+.|+++++||||+|.+.++|++|++  +...|.++.|.|+++.++.
T Consensus        56 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           56 NLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             EECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             EecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            3678899999999999999999999998  5568999999999987653

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.33  E-value=2.4e-07  Score=71.12  Aligned_cols=45  Identities=18%  Similarity=0.285  Sum_probs=39.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+ |+++||||||+|++.++|++||+ +.+.|.++.|.|+++.++
T Consensus        49 ~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           49 LVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             CCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECHH
T ss_pred             EECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEECCHH
Confidence            4677 99999999999999999999998 555889999999887654

>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=98.32  E-value=5.1e-07  Score=70.99  Aligned_cols=47  Identities=21%  Similarity=0.483  Sum_probs=41.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ++|+.|+++|+||||+|++.++|++||+  +...|.++.|.|+++.++.
T Consensus        79 ~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           79 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             ECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            3678899999999999999999999998  5568999999999987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.32  E-value=3.3e-07  Score=72.12  Aligned_cols=48  Identities=21%  Similarity=0.412  Sum_probs=41.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccC----ccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTH----IINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~----~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++||||||+|++. +|++|++  +..    .|.++.|.|+++.++...
T Consensus        58 ~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           58 IKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKRD  111 (131)
T ss_dssp             CBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCCC
T ss_pred             EEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCCC
Confidence            57888999999999999999 9999998  445    789999999998776443

>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=98.32  E-value=4.1e-07  Score=67.12  Aligned_cols=44  Identities=16%  Similarity=0.336  Sum_probs=38.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      |+|+.|+++|+||||+|.++++|++||+  +...|.++.|.|+++.
T Consensus        48 ~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           48 LKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             EEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             EEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            3567899999999999999999999998  5568999999998764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.32  E-value=5.4e-07  Score=65.98  Aligned_cols=45  Identities=18%  Similarity=0.467  Sum_probs=39.3

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~   47 (314)
                      +| .+++++|||||+|.+.++|++||+ +...|.++.|.|+++.++.
T Consensus        43 ~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           43 RN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             EC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEESSCC
T ss_pred             EC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECCcCC
Confidence            45 789999999999999999999999 4448899999999987763

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.31  E-value=1.1e-06  Score=66.19  Aligned_cols=50  Identities=24%  Similarity=0.409  Sum_probs=42.4

Q ss_pred             CCC-CCCCCcccEEEEEECCHHHHHHHHHc---cCccCCcEEEEeecCCCCCCC
Q 021295            1 MKD-RKTGQPRGFGFVTYADPSVVDKVIED---THIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d-~~tg~~kG~aFV~f~~~~~a~~A~~~---~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      ++| +.|+++++||||+|.+.++|++||+.   ...|.++.|.|+++.++....
T Consensus        48 ~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~~  101 (107)
T 2cph_A           48 PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ  101 (107)
T ss_dssp             CCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCCC
T ss_pred             ecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCCC
Confidence            345 67999999999999999999999984   458999999999998775543

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

Probab=98.31  E-value=6.8e-07  Score=66.65  Aligned_cols=46  Identities=20%  Similarity=0.463  Sum_probs=39.8

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      +|+ |+++++||||+|.+.++|++|++  +...|.++.|.|+++.++..
T Consensus        51 ~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           51 TNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             ECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             ECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            455 89999999999999999999997  45589999999999877643

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

Probab=98.31  E-value=3.3e-07  Score=74.56  Aligned_cols=46  Identities=26%  Similarity=0.538  Sum_probs=40.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|.+.++|++||+.  ...|.++.|.|+++.++
T Consensus        90 ~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           90 AENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             EECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            46889999999999999999999999994  46899999999987643

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=98.30  E-value=5.9e-07  Score=67.16  Aligned_cols=46  Identities=9%  Similarity=0.343  Sum_probs=39.6

Q ss_pred             CCCC-CCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            1 MKDR-KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~-~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+ .|+++||||||+|.+.++|++|++ +...|.++.|.|+++.++
T Consensus        51 ~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           51 PREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             SCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEECCCS
T ss_pred             EecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEeccCC
Confidence            3566 599999999999999999999996 455889999999988765

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.30  E-value=7.6e-07  Score=65.49  Aligned_cols=43  Identities=19%  Similarity=0.445  Sum_probs=38.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|+++++||||+|++.++|++|++  +...|.++.|.|+++
T Consensus        49 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           49 MKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             EeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            4678899999999999999999999998  445889999999875

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

Probab=98.30  E-value=8.4e-07  Score=67.36  Aligned_cols=47  Identities=26%  Similarity=0.429  Sum_probs=41.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ++|+.|+++++||||+|.+.++|++|++  +...|.++.|.|+++.++.
T Consensus        59 ~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           59 NLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             CBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             EecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            4678899999999999999999999998  5568999999999987654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.30  E-value=5.3e-07  Score=67.16  Aligned_cols=43  Identities=26%  Similarity=0.516  Sum_probs=38.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|+++||||||+|.+.++|++|++  +...+.++.|.|+++
T Consensus        54 ~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           54 YTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             EECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             EecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            3577899999999999999999999998  556889999999875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.29  E-value=1.5e-07  Score=70.51  Aligned_cols=49  Identities=31%  Similarity=0.615  Sum_probs=40.5

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGS   51 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~   51 (314)
                      +|+ |+++||||||+|++.++|++|+++.+.++++.|.|.++.++.....
T Consensus        43 ~~~-~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~~~~~~~   91 (102)
T 2xs2_A           43 TDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRKQNLST   91 (102)
T ss_dssp             ECT-TSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEECC----
T ss_pred             ECC-CCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCcCcchhh
Confidence            566 9999999999999999999999966689999999999887655443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.29  E-value=1.3e-06  Score=63.53  Aligned_cols=36  Identities=8%  Similarity=0.221  Sum_probs=31.1

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      .+||||||+|.++++|++|++  +..++.+++|.|+.+
T Consensus        41 ~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A           41 LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            489999999999999999999  445888898888754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.29  E-value=6.1e-07  Score=66.10  Aligned_cols=45  Identities=18%  Similarity=0.451  Sum_probs=39.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      ++|+.|+++++||||+|++.++|++|++  +...|.++.|.|+++.+
T Consensus        48 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           48 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             EECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             EEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            3577899999999999999999999998  44588999999988653

>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=98.28  E-value=8.3e-07  Score=69.13  Aligned_cols=49  Identities=20%  Similarity=0.409  Sum_probs=42.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++++||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        55 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           55 NLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP  105 (126)
T ss_dssp             CBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCC
Confidence            4677899999999999999999999997  556899999999998766543

>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=98.27  E-value=5.6e-07  Score=68.39  Aligned_cols=46  Identities=24%  Similarity=0.627  Sum_probs=40.8

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+.|++++|||||+|.+.++|++|++  +...|.++.|.|+++.++.
T Consensus        60 ~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           60 MDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             EETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             EcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            577899999999999999999999998  5568999999999887653

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=98.27  E-value=1.5e-06  Score=70.38  Aligned_cols=49  Identities=22%  Similarity=0.494  Sum_probs=42.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++||||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus       103 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A          103 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             CCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             eecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            4678899999999999999999999998  445899999999998876443

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.27  E-value=7.6e-07  Score=70.58  Aligned_cols=49  Identities=27%  Similarity=0.426  Sum_probs=42.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++|+||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        75 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           75 VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             EEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             EEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            3677899999999999999999999998  445899999999998876544

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.27  E-value=1.5e-06  Score=64.90  Aligned_cols=45  Identities=18%  Similarity=0.547  Sum_probs=39.6

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      .++++|+||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        48 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (101)
T 2fc9_A           48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP   94 (101)
T ss_dssp             SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCC
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCC
Confidence            689999999999999999999998  445889999999998876543

>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=98.27  E-value=7.6e-07  Score=64.14  Aligned_cols=43  Identities=21%  Similarity=0.387  Sum_probs=38.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|+++++||||+|++.++|++|++  +...+.++.|.|+++
T Consensus        40 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           40 PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4577899999999999999999999997  556889999999875

>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=98.27  E-value=6.8e-07  Score=65.00  Aligned_cols=45  Identities=22%  Similarity=0.601  Sum_probs=39.5

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      +|+.|+++++||||+|.+.++|++|++ +...+.++.|.|+++.++
T Consensus        40 ~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           40 CDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             ESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             ecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            567899999999999999999999996 456899999999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.27  E-value=8e-07  Score=67.78  Aligned_cols=44  Identities=20%  Similarity=0.429  Sum_probs=37.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      |+|+ ++++||||||+|+++++|++||+ +.+.|.++.|.|..+.+
T Consensus        48 ~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           48 LKDH-VGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             CCCT-TCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             EECC-CCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            4565 49999999999999999999997 55688999999877654

>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=98.27  E-value=5.5e-07  Score=65.77  Aligned_cols=48  Identities=33%  Similarity=0.657  Sum_probs=37.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++++||||+|++.+ |++|++  +...+.++.|.|+++.++...
T Consensus        34 ~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~~   83 (90)
T 2ki2_A           34 IYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKSL   83 (90)
T ss_dssp             CCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC------
T ss_pred             EEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            467889999999999999999 999998  455889999999998766443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.26  E-value=6e-07  Score=66.79  Aligned_cols=47  Identities=26%  Similarity=0.556  Sum_probs=39.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcE----EEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQ----VEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~----i~v~~~~~~~   47 (314)
                      |+|+.|+++++||||+|.+.++|++|++  +...|.++.    |.|+++.+..
T Consensus        43 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~   95 (99)
T 2div_A           43 IRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSG   95 (99)
T ss_dssp             EECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCS
T ss_pred             eecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCC
Confidence            3578899999999999999999999999  445788888    8888876543

>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=98.26  E-value=1e-06  Score=71.32  Aligned_cols=48  Identities=13%  Similarity=0.201  Sum_probs=41.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+.|+++|+||||+|++.++|++||+  +.+.|.++.|.|+++.+...
T Consensus        72 ~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           72 GLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            3678899999999999999999999998  55689999999999976543

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

Probab=98.26  E-value=8.9e-07  Score=66.46  Aligned_cols=48  Identities=27%  Similarity=0.601  Sum_probs=40.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--Cc-cCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HI-INGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~-i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+ |+++|+||||+|.+.++|++||+.+  .. |.++.|.|+++.++...
T Consensus        43 ~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   93 (104)
T 2dhg_A           43 VLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASR   93 (104)
T ss_dssp             EECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSC
T ss_pred             EECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcC
Confidence            3566 9999999999999999999999944  46 89999999998776544

>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=98.25  E-value=1.4e-06  Score=67.02  Aligned_cols=47  Identities=26%  Similarity=0.577  Sum_probs=40.4

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      +|+ |+++++||||+|++.++|++|++  +...|.++.|.|+++.++...
T Consensus        41 ~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           41 KDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             CST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSCS
T ss_pred             ECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            455 99999999999999999999998  455899999999998766543

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

Probab=98.25  E-value=4.8e-07  Score=63.94  Aligned_cols=43  Identities=42%  Similarity=0.723  Sum_probs=37.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc-CccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~-~~i~g~~i~v~~~   43 (314)
                      ++|+.|++++|||||+|.+.++|++|++.+ ..+.++.|.|+++
T Consensus        33 ~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a   76 (77)
T 1uaw_A           33 MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             ECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             ecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            357789999999999999999999999933 6889999999876

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

Probab=98.24  E-value=1e-06  Score=69.81  Aligned_cols=49  Identities=22%  Similarity=0.494  Sum_probs=42.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++||||||+|.+.++|++||+  +...|.++.|.|+++.+....
T Consensus        80 ~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            4677899999999999999999999998  456899999999998876544

>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=98.24  E-value=2.6e-07  Score=72.40  Aligned_cols=45  Identities=20%  Similarity=0.372  Sum_probs=38.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+. +++||||||+|+++++|++||+ +...|.++.|.|..+.++
T Consensus        76 ~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a~~~  121 (126)
T 2hgm_A           76 PVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE  121 (126)
T ss_dssp             CCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEECHH
T ss_pred             EECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCHH
Confidence            45665 9999999999999999999998 446888999998877544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.23  E-value=8.5e-07  Score=65.83  Aligned_cols=45  Identities=24%  Similarity=0.508  Sum_probs=39.0

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+++++||||+|.+.++|++|++  +...|.++.|.|+++.++....
T Consensus        46 t~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   92 (98)
T 2cpf_A           46 VLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPA   92 (98)
T ss_dssp             CEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCCC
T ss_pred             CcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCCC
Confidence            66999999999999999999999  4568999999999987765443

>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=98.23  E-value=3.3e-07  Score=71.37  Aligned_cols=45  Identities=11%  Similarity=0.294  Sum_probs=38.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      |+|+.|+++||||||+|++.++|++||+ +.+.|.++.|.|.++.+
T Consensus        58 ~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           58 IAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             EEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECH
T ss_pred             EEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCH
Confidence            3566899999999999999999999999 44588999999987754

>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=98.22  E-value=7.9e-07  Score=66.70  Aligned_cols=46  Identities=24%  Similarity=0.598  Sum_probs=40.3

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+.|+++++||||+|.+.++|++|++  +...|.++.|.|+++.++.
T Consensus        42 ~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   89 (104)
T 1p1t_A           42 YDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             EETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             eCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCcc
Confidence            567899999999999999999999998  4558899999999887653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.20  E-value=2.6e-06  Score=66.16  Aligned_cols=47  Identities=17%  Similarity=0.274  Sum_probs=40.5

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      +|+ |+++++||||+|++.++|++|++  +...|.++.|.|+++.++...
T Consensus        69 ~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  117 (124)
T 2kt5_A           69 YDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL  117 (124)
T ss_dssp             CCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTCC
T ss_pred             ECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCC
Confidence            466 89999999999999999999998  455899999999998776443

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

Probab=98.20  E-value=1.4e-06  Score=66.71  Aligned_cols=44  Identities=18%  Similarity=0.308  Sum_probs=37.3

Q ss_pred             CCCCCC---CCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecC
Q 021295            1 MKDRKT---GQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI   44 (314)
Q Consensus         1 m~d~~t---g~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~   44 (314)
                      |+|+.|   +++||||||+|+++++|++||+.++.++++.+.+..+.
T Consensus        40 ~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~~~~   86 (114)
T 2dnl_A           40 PHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSP   86 (114)
T ss_dssp             TTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEECCS
T ss_pred             eecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEeccCC
Confidence            355566   79999999999999999999998878899998887543

>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=98.18  E-value=2.1e-06  Score=65.41  Aligned_cols=43  Identities=16%  Similarity=0.325  Sum_probs=37.2

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      +.+++|||||+|+++++|++||+  +...|.++.|.|+++.++..
T Consensus        59 ~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           59 SQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC  103 (111)
T ss_dssp             SSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCSC
T ss_pred             cCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEecccccc
Confidence            34677999999999999999999  45589999999999887753

>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=98.17  E-value=2.2e-06  Score=64.37  Aligned_cols=47  Identities=13%  Similarity=0.217  Sum_probs=39.2

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCC---cEEEEeecCCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIING---KQVEIKRTIPKGAV   49 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g---~~i~v~~~~~~~~~   49 (314)
                      +|+ |+++|+||||+|.+.++|++||+  +...+.+   +.|.|+++.++...
T Consensus        49 ~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           49 RGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES  100 (105)
T ss_dssp             ECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCC
T ss_pred             ECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCccc
Confidence            455 89999999999999999999998  4456777   99999998876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.17  E-value=2.7e-06  Score=63.71  Aligned_cols=45  Identities=24%  Similarity=0.493  Sum_probs=39.7

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      ++++++||||+|.+.++|++||+  +...|.++.|.|+++.++....
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2d9p_A           51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ   97 (103)
T ss_dssp             SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCCC
T ss_pred             CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccCC
Confidence            88999999999999999999998  5568999999999998775543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.17  E-value=2.2e-06  Score=66.51  Aligned_cols=46  Identities=20%  Similarity=0.572  Sum_probs=40.1

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+.|+++++||||+|.+.++|++||+ +.+.|.++.|.|+++.+..
T Consensus        70 ~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~  116 (124)
T 2jwn_A           70 CDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNM  116 (124)
T ss_dssp             EECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSCCC
T ss_pred             ecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCCCC
Confidence            567899999999999999999999996 4458999999999887543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.16  E-value=3.1e-06  Score=64.52  Aligned_cols=45  Identities=20%  Similarity=0.379  Sum_probs=38.5

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+ ++++++||||+|++.++|++||+  +.+.|.++.|.|+++....
T Consensus        49 ~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   95 (114)
T 2do0_A           49 EDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL   95 (114)
T ss_dssp             ECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCC
T ss_pred             ECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCC
Confidence            454 69999999999999999999998  5568999999999876543

>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=98.15  E-value=7.9e-07  Score=76.94  Aligned_cols=45  Identities=18%  Similarity=0.385  Sum_probs=39.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~   45 (314)
                      |+|+.|+++||||||+|++.++|++||+.  .+.|.++.|.|+++.+
T Consensus       103 ~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C          103 FENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             EECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            46889999999999999999999999984  4588999999987653

>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=98.15  E-value=3.3e-06  Score=62.54  Aligned_cols=44  Identities=7%  Similarity=-0.028  Sum_probs=36.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ++|+.|   |+||||+|++.++|++|++  +...|.++.|.|+++.+..
T Consensus        46 ~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           46 SPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             CSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             EeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            355555   8999999999999999998  4458999999999987654

>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=98.15  E-value=9.5e-07  Score=67.56  Aligned_cols=46  Identities=15%  Similarity=0.370  Sum_probs=40.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++++||||+|.+.++|++||. +.+.|.++.|.|+++.++
T Consensus        58 ~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           58 ISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             CCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             EecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCCC
Confidence            4688899999999999999999999995 455889999999987654

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

Probab=98.14  E-value=1.5e-06  Score=66.84  Aligned_cols=43  Identities=21%  Similarity=0.518  Sum_probs=37.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      |+|+.|+++|+||||+|.+.++|++|++  +...|.++.|.|+++
T Consensus        73 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           73 FIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             EeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            4678899999999999999999999998  455889999988875

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

Probab=98.13  E-value=1.7e-06  Score=65.13  Aligned_cols=43  Identities=14%  Similarity=0.094  Sum_probs=37.1

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      +|+. +++||||||+|+++++|++||+ +.+.|.++.|.|+++..
T Consensus        45 ~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           45 RTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             CCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHHH
T ss_pred             ECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEchH
Confidence            5665 9999999999999999999999 45689999999987643

>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=98.13  E-value=9.8e-07  Score=70.03  Aligned_cols=43  Identities=19%  Similarity=0.334  Sum_probs=36.7

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      +|+. +++||||||+|+++++|++||+ +...|.++.|+|.++.+
T Consensus        81 ~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A           81 YTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHR  124 (136)
T ss_dssp             ECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEEECCH
T ss_pred             ECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEEECCh
Confidence            4665 9999999999999999999998 44588999999887643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.13  E-value=4.8e-07  Score=70.57  Aligned_cols=42  Identities=19%  Similarity=0.402  Sum_probs=35.0

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      +| .|+++||||||+|+++++|++||+ +.+.|.++.|+|..+.
T Consensus        61 ~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~~a~  103 (123)
T 2dha_A           61 TY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRST  103 (123)
T ss_dssp             EC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCEEEC
T ss_pred             EC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEEECC
Confidence            45 599999999999999999999998 4457788888776553

>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=98.12  E-value=8.3e-07  Score=70.72  Aligned_cols=47  Identities=17%  Similarity=0.169  Sum_probs=39.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+. +++||||||+|+++++|++||+ +.+.|.++.|+|..+.+++.
T Consensus        78 ~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           78 EIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSCC
T ss_pred             EECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCCC
Confidence            46764 9999999999999999999997 55688999999988776543

>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=98.11  E-value=2.2e-06  Score=62.05  Aligned_cols=45  Identities=18%  Similarity=0.530  Sum_probs=38.3

Q ss_pred             CCCCCCC-cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            2 KDRKTGQ-PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         2 ~d~~tg~-~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +|+.|+. +++||||+|.+.++|++|++  +...+.++.|.|+++.+.
T Consensus        38 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   85 (88)
T 4a8x_A           38 VERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAP   85 (88)
T ss_dssp             EETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCC
T ss_pred             eCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCC
Confidence            4555555 99999999999999999998  566899999999988765

>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=98.11  E-value=2.4e-06  Score=64.39  Aligned_cols=42  Identities=19%  Similarity=0.318  Sum_probs=37.2

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      +|+ |+++++||||+|.+.++|++|++  +...|.++.|.|+++.
T Consensus        63 ~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           63 YDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             ECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             ECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            455 99999999999999999999999  5568899999998864

>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=98.10  E-value=1.7e-06  Score=65.46  Aligned_cols=44  Identities=20%  Similarity=0.334  Sum_probs=36.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      |+|+. +++||||||+|++.++|++||+ +.+.|.++.|.|.++.+
T Consensus        47 ~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           47 LLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             CCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCEECCH
T ss_pred             EECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEEECCH
Confidence            35665 9999999999999999999998 44578888888877653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.10  E-value=9.5e-07  Score=63.72  Aligned_cols=42  Identities=21%  Similarity=0.493  Sum_probs=34.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEee
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKR   42 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~   42 (314)
                      ++|+.|+++++||||+|++.++|++|++.  ...|.++.|++.+
T Consensus        38 ~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A           38 ILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             ECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             EecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            36778999999999999999999999984  3466776666554

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

Probab=97.38  E-value=4e-07  Score=69.96  Aligned_cols=49  Identities=22%  Similarity=0.463  Sum_probs=42.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++|+||||+|++.++|++|++  +...|.++.|.|+++.++...
T Consensus        48 ~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           48 YTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            3567899999999999999999999998  455889999999998776543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.09  E-value=1.9e-06  Score=66.57  Aligned_cols=43  Identities=19%  Similarity=0.325  Sum_probs=36.4

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      +|+. +++||||||+|++.++|++||+ +.+.|.++.|.|.++.+
T Consensus        54 ~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~   97 (118)
T 2db1_A           54 YTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHR   97 (118)
T ss_dssp             ECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEEEECH
T ss_pred             ECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCH
Confidence            4554 9999999999999999999998 44588999999887643

>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=98.09  E-value=6.1e-06  Score=61.69  Aligned_cols=43  Identities=23%  Similarity=0.598  Sum_probs=37.4

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      .+++||||+|.+.++|++||+  +...|.++.|.|+++.++....
T Consensus        53 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cq3_A           53 GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTN   97 (103)
T ss_dssp             TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCCC
T ss_pred             CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCCC
Confidence            489999999999999999998  4558999999999998775544

>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=98.09  E-value=6.2e-06  Score=61.65  Aligned_cols=42  Identities=14%  Similarity=0.264  Sum_probs=36.2

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      .+|+||||+|.+.++|++|++  +...|.++.|.|+++.++...
T Consensus        53 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           53 SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence            379999999999999999998  445889999999998876543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.08  E-value=5.2e-06  Score=62.19  Aligned_cols=42  Identities=10%  Similarity=0.135  Sum_probs=37.2

Q ss_pred             CCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~   48 (314)
                      +++||||||+|++.++|++||+..+.+.++.|.|+++.++..
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            478999999999999999999988888899999999876643

>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=98.07  E-value=3.1e-06  Score=64.69  Aligned_cols=46  Identities=22%  Similarity=0.296  Sum_probs=39.8

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ..|+++|+||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        61 ~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  108 (115)
T 2cpx_A           61 MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  108 (115)
T ss_dssp             EECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             cCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCC
Confidence            3489999999999999999999998  455889999999998876544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.05  E-value=4e-06  Score=63.17  Aligned_cols=44  Identities=16%  Similarity=0.366  Sum_probs=38.0

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCc-EEEEeecCCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGK-QVEIKRTIPKG   47 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~-~i~v~~~~~~~   47 (314)
                      +.|+++||||||+|.+.++|++|++  +...|.++ .|.|+++...+
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            4689999999999999999999999  44588998 99999876543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.04  E-value=3.7e-06  Score=65.84  Aligned_cols=44  Identities=11%  Similarity=0.206  Sum_probs=38.2

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +.|+++||||||+|.+.++|++|++  +...|.++.|.|+++.++.
T Consensus        66 ~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           66 DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ  111 (127)
T ss_dssp             CCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCC
T ss_pred             ccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcc
Confidence            3578999999999999999999998  4558899999999987653

>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=98.04  E-value=6.7e-06  Score=62.20  Aligned_cols=44  Identities=16%  Similarity=0.269  Sum_probs=38.0

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      .+.++|+||||+|++.++|++||+  +...|.++.|.|+++.++..
T Consensus        56 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  101 (109)
T 1x4a_A           56 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG  101 (109)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCC
T ss_pred             ECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCC
Confidence            466789999999999999999997  55689999999999877644

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

Probab=98.04  E-value=4.8e-06  Score=60.85  Aligned_cols=44  Identities=16%  Similarity=0.527  Sum_probs=38.5

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      .++++|+||||+|.+.++|++|++  +...|.++.|.|+++.+...
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            478999999999999999999998  55689999999999877644

>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=98.03  E-value=3.4e-06  Score=68.99  Aligned_cols=49  Identities=24%  Similarity=0.402  Sum_probs=41.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++++||||+|.+.++|++||+  +...|.++.|.|.++.++...
T Consensus       105 ~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A          105 NLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             EECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             EecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            3577899999999999999999999998  455899999999998766543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.01  E-value=6e-06  Score=60.87  Aligned_cols=44  Identities=23%  Similarity=0.502  Sum_probs=38.3

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~~~   48 (314)
                      .+++++|||||+|.+.++|++|++.  ...|.++.|.|+++.++..
T Consensus        48 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            5789999999999999999999994  4488999999999876643

>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=98.01  E-value=4e-06  Score=61.66  Aligned_cols=42  Identities=31%  Similarity=0.668  Sum_probs=36.2

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      +|+ ++++|+||||+|+++++|++|++  +...|.++.|.|+++.
T Consensus        50 ~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           50 KDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             ECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             ECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            354 48999999999999999999998  5568999999998764

>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=97.97  E-value=3.2e-06  Score=67.30  Aligned_cols=45  Identities=16%  Similarity=0.316  Sum_probs=39.1

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      +.|++++|||||+|.+.++|++||+  +...|.++.|.|+++.+...
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            4689999999999999999999998  45589999999999876543

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.97  E-value=6.3e-05  Score=54.98  Aligned_cols=69  Identities=6%  Similarity=0.229  Sum_probs=56.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCC--cceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR--SRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~--~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      .+|.|++||..+||+++.+.+....++.....+.-+.+.+  .-.-|+|.|++.+++.+..+.+++..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            5789999999999999999999988777776665543322  23469999999999999999999877654

>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=97.97  E-value=3.2e-05  Score=57.59  Aligned_cols=75  Identities=15%  Similarity=0.218  Sum_probs=63.7

Q ss_pred             cceEEEcCCCCCC-C----HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           56 TKKIFVGGIPSSV-N----EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        56 ~~~l~V~nLp~~~-~----e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      +++|+|.||+.++ +    .++|+++|.+|.++.....++.-     | =..|.|.++++|.+|-..||...+.+++|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----R-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----K-RVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----T-EEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----e-EEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            5789999998876 2    25778999999999888777652     2 4799999999999999999999999999999


Q ss_pred             eecCCC
Q 021295          131 KKAEPK  136 (314)
Q Consensus       131 ~~a~~~  136 (314)
                      -++.+.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998754

>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=97.95  E-value=8e-06  Score=62.24  Aligned_cols=43  Identities=26%  Similarity=0.426  Sum_probs=33.6

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHc--cCcc--------CCcEEEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIED--THII--------NGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i--------~g~~i~v~~~~~   45 (314)
                      +|+ |+++|+||||+|.+.++|++|++.  ...|        .++.|.|+++.+
T Consensus        59 ~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           59 RDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGP  111 (114)
T ss_dssp             ECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCC
T ss_pred             ECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCC
Confidence            466 899999999999999999999983  3345        456666666654

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.94  E-value=1.3e-05  Score=61.11  Aligned_cols=43  Identities=23%  Similarity=0.373  Sum_probs=36.8

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      .+||||||+|.+.++|++|++  +...|.++.|.|+++.++....
T Consensus        62 ~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           62 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCCSS
T ss_pred             CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCcc
Confidence            489999999999999999998  4458899999999988765443

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=97.93  E-value=8e-06  Score=61.71  Aligned_cols=44  Identities=9%  Similarity=-0.019  Sum_probs=36.9

Q ss_pred             CCCC-CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            2 KDRK-TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~-tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      +|+. +++++|||||+|+++++|++|++  +...+.++.|.+.++.+
T Consensus        47 ~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           47 EIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             ECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            4544 47899999999999999999998  45589999999988754

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=97.93  E-value=5.5e-06  Score=59.14  Aligned_cols=37  Identities=16%  Similarity=0.485  Sum_probs=30.6

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHHc--cCccCCc-EEEE
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIED--THIINGK-QVEI   40 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~-~i~v   40 (314)
                      +.|+++||||||+|.+.++|++|++.  ...+.++ +|.|
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            46899999999999999999999994  3467776 6654

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

Probab=97.90  E-value=1.3e-05  Score=58.90  Aligned_cols=46  Identities=20%  Similarity=0.398  Sum_probs=37.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|++   ||||+|.+.++|++||+ +.+.|.++.|.|+++.++...
T Consensus        39 ~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~~~~~   85 (94)
T 2e5g_A           39 VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEFQ   85 (94)
T ss_dssp             EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCCSCCC
T ss_pred             EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCcCCCC
Confidence            35666776   99999999999999999 445889999999987765443

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=97.89  E-value=1.2e-05  Score=61.47  Aligned_cols=41  Identities=15%  Similarity=0.286  Sum_probs=35.0

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +.++||||||+|++.++|++||+  +..+|.++.|.|+++...
T Consensus        63 ~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           63 TRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             SCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             cCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            34689999999999999999998  445899999999987654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.89  E-value=9.9e-06  Score=59.92  Aligned_cols=42  Identities=12%  Similarity=0.249  Sum_probs=36.7

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +.++++||||+|.+.++|++|++  +...|.++.|.|+++.++.
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            55789999999999999999997  5568999999999987654

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

Probab=97.87  E-value=1.2e-05  Score=60.69  Aligned_cols=42  Identities=10%  Similarity=0.190  Sum_probs=35.4

Q ss_pred             cccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~~   50 (314)
                      .||||||+|+++++|++|++.+    .+|.+++|.|+++.++....
T Consensus        51 ~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           51 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence            4899999999999999999832    47899999999988765544

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.87  E-value=2.2e-05  Score=57.97  Aligned_cols=43  Identities=19%  Similarity=0.367  Sum_probs=36.7

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      .++|+||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        46 ~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML   90 (97)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCC
Confidence            3689999999999999999998  445889999999998776543

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=97.86  E-value=1.2e-05  Score=60.64  Aligned_cols=38  Identities=13%  Similarity=0.261  Sum_probs=33.3

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      ++++||||||+|+++++|++|++  +...+.++.|.|+++
T Consensus        64 ~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           64 GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            57899999999999999999998  455889999988764

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

Probab=97.85  E-value=1.4e-05  Score=60.51  Aligned_cols=40  Identities=25%  Similarity=0.664  Sum_probs=35.4

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      ..+|+||||+|++.++|++|++  +...|.++.|.|+++.++
T Consensus        66 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           66 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3589999999999999999998  556899999999998765

>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=97.83  E-value=2.3e-05  Score=57.35  Aligned_cols=42  Identities=26%  Similarity=0.440  Sum_probs=36.3

Q ss_pred             CcccEEEEEECCHHHHHHHHH--cc-CccCCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DT-HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~-~~i~g~~i~v~~~~~~~~~   49 (314)
                      .+++||||+|++.++|++|++  +. ..|.++.|.|+++.++...
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            479999999999999999998  44 6799999999998876543

>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=97.82  E-value=1.5e-05  Score=60.82  Aligned_cols=43  Identities=7%  Similarity=0.113  Sum_probs=36.0

Q ss_pred             CcccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~~   50 (314)
                      ++|+||||+|++.++|++|++.+    ..|.+++|.|.++..+....
T Consensus        60 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~~~  106 (112)
T 1x4f_A           60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLV  106 (112)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSSSS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccccc
Confidence            57899999999999999999833    35899999999987765443

>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=97.81  E-value=1.8e-05  Score=74.82  Aligned_cols=47  Identities=21%  Similarity=0.537  Sum_probs=41.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |+|+.|++++|||||+|.+.++|++||+  +.+.|.++.|.|+++.++.
T Consensus       135 ~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          135 VYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             eccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            4678899999999999999999999997  4568999999999987653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=97.80  E-value=7.6e-06  Score=63.73  Aligned_cols=43  Identities=16%  Similarity=0.210  Sum_probs=33.8

Q ss_pred             CCCCCCCCcccEEEEEECC----HHH----HHHHHH----ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYAD----PSV----VDKVIE----DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~----~~~----a~~A~~----~~~~i~g~~i~v~~~   43 (314)
                      |+|++|++|+|||||+|.+    +++    |.+|++    +...|++++|.|+..
T Consensus        39 i~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln   93 (136)
T 2j8a_A           39 FNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILN   93 (136)
T ss_dssp             EECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEEC
T ss_pred             EecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEEC
Confidence            5799999999999999996    332    677776    455889999998854

>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=97.79  E-value=2.8e-05  Score=56.39  Aligned_cols=40  Identities=15%  Similarity=0.232  Sum_probs=34.8

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ++||||||+|.++++|++|++  +...+.+++|.|+++....
T Consensus        38 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A           38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            689999999999999999998  4458899999999886554

>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=97.77  E-value=1.2e-05  Score=59.30  Aligned_cols=42  Identities=17%  Similarity=0.249  Sum_probs=36.9

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |+++++||||+|.+.++|++|++  +...+.++.|.|+++.++.
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           47 SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCC
Confidence            56789999999999999999998  5568899999999987654

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

Probab=97.77  E-value=3.7e-05  Score=57.42  Aligned_cols=40  Identities=10%  Similarity=0.148  Sum_probs=33.6

Q ss_pred             CcccEEEEEECCHHHHHHHHHcc--C--ccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDT--H--IINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~--~--~i~g~~i~v~~~~~~~   47 (314)
                      ++|+||||+|++.++|++|++.+  .  .|.+++|.|..+.+++
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            46899999999999999999833  2  3789999999987653

>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=97.75  E-value=5e-05  Score=56.84  Aligned_cols=42  Identities=12%  Similarity=0.110  Sum_probs=35.1

Q ss_pred             cccEEEEEECCHHHHHHHHHc----cCccCCcEEEEeecCCCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIED----THIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~----~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      .|+||||+|++.++|++|++.    ...|.+++|.|+++.++....
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           50 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCcC
Confidence            489999999999999999983    246899999999988765443

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=97.75  E-value=3.9e-05  Score=57.87  Aligned_cols=38  Identities=16%  Similarity=0.060  Sum_probs=33.4

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      .+++|||||+|+++++|++|++  +...+.++.|.+....
T Consensus        56 ~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           56 VPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             CTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             cCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            5789999999999999999998  4458899999998754

>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=97.74  E-value=1.6e-05  Score=58.94  Aligned_cols=42  Identities=19%  Similarity=0.449  Sum_probs=35.9

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+||||+|++.++|++|++  +...|.++.|.|+++.++...
T Consensus        49 ~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~   92 (99)
T 2cpj_A           49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL   92 (99)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCCC
Confidence            468999999999999999997  455899999999998876443

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

Probab=97.73  E-value=4.3e-05  Score=55.49  Aligned_cols=40  Identities=18%  Similarity=0.439  Sum_probs=34.8

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+||||+|.+.++|++|++  +...|.++.|.|+++.++...
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            7999999999999999997  445799999999998876543

>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=97.72  E-value=4e-05  Score=57.49  Aligned_cols=42  Identities=12%  Similarity=0.171  Sum_probs=34.7

Q ss_pred             CcccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~   49 (314)
                      +.|+||||+|++.++|++|++.+    .+|.+++|.|.++.++...
T Consensus        50 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~   95 (102)
T 1x4d_A           50 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRI   95 (102)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTTS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCCC
Confidence            35799999999999999999832    3589999999998865443

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.71  E-value=6.1e-05  Score=55.71  Aligned_cols=41  Identities=15%  Similarity=0.444  Sum_probs=35.5

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      .+|+||||+|.+.++|++|++  +...|.++.|.|+++.++..
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            458999999999999999998  45588999999999887654

>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=97.70  E-value=6.8e-05  Score=56.41  Aligned_cols=41  Identities=12%  Similarity=0.139  Sum_probs=34.5

Q ss_pred             cccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~   49 (314)
                      .|+||||+|++.++|++|++.+    ..|.+++|.|+++.++...
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            4899999999999999999832    3589999999998776543

>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=97.69  E-value=6.3e-05  Score=56.12  Aligned_cols=42  Identities=17%  Similarity=0.358  Sum_probs=35.8

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      .|+||||+|.+.++|++||+  +.+.|.++.|.|+++.++....
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            47799999999999999998  4558999999999988765544

>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=97.69  E-value=3.8e-05  Score=59.28  Aligned_cols=42  Identities=10%  Similarity=0.190  Sum_probs=35.7

Q ss_pred             cccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~~   50 (314)
                      .|+||||+|++.++|++|++.+    ..|.+++|.|+++.++....
T Consensus        66 ~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           66 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            4899999999999999999833    46999999999988765544

>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=97.68  E-value=0.00017  Score=55.10  Aligned_cols=75  Identities=16%  Similarity=0.257  Sum_probs=59.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC-eEEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG-AQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g-r~l~V  130 (314)
                      +....+.|.|-.+|.+. ...|.++|++||+|+++....      ..-...|.|+++.+|++||.+ |+..|.+ ..|-|
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV   91 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGV   91 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEE
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEE
Confidence            44567889999999885 577889999999999888732      234899999999999999999 8888875 66677


Q ss_pred             eecC
Q 021295          131 KKAE  134 (314)
Q Consensus       131 ~~a~  134 (314)
                      +++.
T Consensus        92 ~p~~   95 (119)
T 1wwh_A           92 KPCI   95 (119)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            6654

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

Probab=97.67  E-value=1.5e-05  Score=59.24  Aligned_cols=38  Identities=13%  Similarity=0.227  Sum_probs=33.4

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      ++|+||||+|.+.++|++|++  +...|.++.|.|+++.+
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            679999999999999999997  55688999999988765

>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=97.63  E-value=8.9e-05  Score=55.90  Aligned_cols=40  Identities=18%  Similarity=0.323  Sum_probs=35.2

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+||||+|.+.++|++|++  +...|.++.|.|+++.++...
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            8999999999999999997  556899999999998876544

>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=97.62  E-value=0.00014  Score=53.19  Aligned_cols=54  Identities=19%  Similarity=0.394  Sum_probs=44.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG  118 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l  118 (314)
                      .+.++| .+|.++...||.++|+.|+.|. |+.+.|  |     .|||.|.+++.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidD--T-----sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcC--C-----eEEEEecCHHHHHHHHHhc
Confidence            345555 9999999999999999999554 555555  3     7999999999999999865

>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=97.62  E-value=2.3e-05  Score=56.42  Aligned_cols=36  Identities=22%  Similarity=0.532  Sum_probs=30.5

Q ss_pred             CCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEee
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR   42 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~   42 (314)
                      .++|+||||+|.+.++|++|+. +...+.++.|.|++
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            3569999999999999999995 44578899988875

>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=97.61  E-value=6.6e-05  Score=55.30  Aligned_cols=38  Identities=5%  Similarity=0.214  Sum_probs=33.6

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccC--CcEEEEeecCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIIN--GKQVEIKRTIPKG   47 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~--g~~i~v~~~~~~~   47 (314)
                      |+||||+|++.++|++|++  +...|.  ++.|.|+++.++.
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            8999999999999999998  455788  8999999988764

>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=97.60  E-value=4.6e-05  Score=55.47  Aligned_cols=40  Identities=38%  Similarity=0.562  Sum_probs=31.4

Q ss_pred             CcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~   47 (314)
                      .+||||||+|+++++|+++......+.++.|.|+++.++.
T Consensus        46 ~srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           46 PFRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             SCCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEECC---
T ss_pred             CCCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEEcCCCC
Confidence            3899999999999999976555556779999999987764

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.57  E-value=0.00012  Score=53.38  Aligned_cols=41  Identities=15%  Similarity=0.307  Sum_probs=35.1

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      ++||||+|++.++|++|++  +.+.|.++.|.|+++.++....
T Consensus        44 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   86 (92)
T 2dgt_A           44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA   86 (92)
T ss_dssp             SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCCC
Confidence            5699999999999999998  5568999999999998765543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.56  E-value=0.00026  Score=52.06  Aligned_cols=72  Identities=4%  Similarity=0.121  Sum_probs=52.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCC--cceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR--SRGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~--~rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ..+-+|.|+.||+.+||+++.+.+...-++.....+.-..+-+  .-.-|+|.|++.+++....+..++..+.+
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            3567899999999999999999888765543333322222211  12358999999999999999999988754

>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=97.56  E-value=9.8e-05  Score=54.59  Aligned_cols=38  Identities=24%  Similarity=0.525  Sum_probs=33.0

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +|+||||+|.+.++|++|++  +...+.++.|.|+++.++
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            48999999999999999998  445788999999987654

>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=97.55  E-value=6.7e-05  Score=56.68  Aligned_cols=40  Identities=15%  Similarity=0.414  Sum_probs=34.6

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      +|+||||+|++.++|++|++  +...|.++.|.|+++.+...
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP  102 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCCS
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCCC
Confidence            68999999999999999997  55689999999999875433

>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=97.54  E-value=4e-05  Score=55.43  Aligned_cols=42  Identities=33%  Similarity=0.524  Sum_probs=35.5

Q ss_pred             CcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      .+|+||||+|++.++|++|+.....+.+++|.|.++.++...
T Consensus        40 ~~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           40 PFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             SCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCCC
T ss_pred             CCCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCCCCCC
Confidence            379999999999999998877666779999999988876544

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

Probab=97.54  E-value=6.2e-05  Score=55.41  Aligned_cols=41  Identities=22%  Similarity=0.472  Sum_probs=34.5

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      +|+||||+|.+.++|++|++  +...+.++.|.|+++.++...
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   86 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARP   86 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC-
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCCC
Confidence            58999999999999999998  445888999999998765443

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

Probab=97.52  E-value=0.00011  Score=53.82  Aligned_cols=35  Identities=9%  Similarity=0.115  Sum_probs=31.5

Q ss_pred             EEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295           13 GFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus        13 aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |||+|.+.++|++|++  +...|.++.|.|+++.+++
T Consensus        57 afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           57 VNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            9999999999999998  5568999999999988774

>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=97.51  E-value=0.00016  Score=58.82  Aligned_cols=42  Identities=14%  Similarity=0.095  Sum_probs=34.7

Q ss_pred             CCcccEEEEEECCHHHHHHHHHcc--CccCC--cEEEEeecCCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIEDT--HIING--KQVEIKRTIPKGA   48 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~~~--~~i~g--~~i~v~~~~~~~~   48 (314)
                      .++++||||+|++.++|++|++.+  ..|.+  +.|+|+++.++..
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            347899999999999999999944  47754  8999999887653

>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=97.49  E-value=0.00014  Score=54.75  Aligned_cols=40  Identities=13%  Similarity=0.208  Sum_probs=34.0

Q ss_pred             cEEEEEECCHHHHHHHHHcc--CccCC-----cEEEEeecCCCCCCC
Q 021295           11 GFGFVTYADPSVVDKVIEDT--HIING-----KQVEIKRTIPKGAVG   50 (314)
Q Consensus        11 G~aFV~f~~~~~a~~A~~~~--~~i~g-----~~i~v~~~~~~~~~~   50 (314)
                      +||||+|++.++|++||+.+  .+|.+     +.|.|+++.++....
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~~~   97 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY   97 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSCCC
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCCCC
Confidence            89999999999999999944  47788     999999988765543

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

Probab=97.49  E-value=0.00016  Score=52.36  Aligned_cols=39  Identities=13%  Similarity=0.334  Sum_probs=34.0

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      ++||||+|.+.++|++|++  +...|.++.|.|+++.+...
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            5699999999999999998  55689999999999877643

>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=97.48  E-value=0.00015  Score=55.07  Aligned_cols=39  Identities=8%  Similarity=0.020  Sum_probs=34.1

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      ++|+||||+|.+.++|++|++  +...|.++.|.|+++...
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            478999999999999999998  455889999999997654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.48  E-value=0.00017  Score=52.89  Aligned_cols=40  Identities=5%  Similarity=0.144  Sum_probs=34.7

Q ss_pred             cEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCC
Q 021295           11 GFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus        11 G~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|||+|.+.++|++|++  +..++.+++|+|..+..+.+..
T Consensus        47 G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd~~   88 (96)
T 2diu_A           47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELC   88 (96)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCCCC
T ss_pred             CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCccee
Confidence            999999999999999998  5568999999999987765543

>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=97.45  E-value=0.00011  Score=52.46  Aligned_cols=36  Identities=22%  Similarity=0.474  Sum_probs=31.1

Q ss_pred             CcccEEEEEECCHHHHHHHHHcc---CccCCcEEEEeec
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDT---HIINGKQVEIKRT   43 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~---~~i~g~~i~v~~~   43 (314)
                      ++|+||||+|++.++|++|++.+   ..+.++.|.|+++
T Consensus        46 ~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           46 QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            36899999999999999999844   5788999988875

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

Probab=97.44  E-value=0.00012  Score=55.22  Aligned_cols=38  Identities=21%  Similarity=0.398  Sum_probs=33.8

Q ss_pred             ccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295           10 RGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus        10 kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |+||||+|.+.++|++|++  +...|.++.|.|+++.++.
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            8999999999999999998  5568899999999987654

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=97.41  E-value=0.00014  Score=56.06  Aligned_cols=39  Identities=18%  Similarity=0.125  Sum_probs=34.1

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      |++++||+||+|+++++|++|++  +...+.++.|.+....
T Consensus        67 ~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           67 DAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             TCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            57889999999999999999999  4458899999998754

>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=97.36  E-value=0.0003  Score=51.66  Aligned_cols=54  Identities=17%  Similarity=0.390  Sum_probs=44.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN  119 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~  119 (314)
                      ..++| .+|.++...||.++|+.||.| .|..+.|  |     .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD--T-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD--T-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET--T-----EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC--C-----eEEEEecCHHHHHHHHHhcc
Confidence            34455 999999999999999999844 4555555  3     79999999999999999764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=97.34  E-value=0.00026  Score=55.36  Aligned_cols=40  Identities=20%  Similarity=0.244  Sum_probs=33.1

Q ss_pred             cccE-EEEEECCHHHHHHHHH--ccCccCC--cEEEEeecCCCCC
Q 021295            9 PRGF-GFVTYADPSVVDKVIE--DTHIING--KQVEIKRTIPKGA   48 (314)
Q Consensus         9 ~kG~-aFV~f~~~~~a~~A~~--~~~~i~g--~~i~v~~~~~~~~   48 (314)
                      +|+| |||+|+++++|++|++  +...|.+  +.|+|+++.++..
T Consensus        64 ~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           64 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            4788 9999999999999999  4457776  8899998877644

>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=97.31  E-value=0.00026  Score=54.09  Aligned_cols=37  Identities=5%  Similarity=0.109  Sum_probs=27.1

Q ss_pred             cccEEEEEECCHHHHHHHHHccC--cc-----CCcEEEEeecCC
Q 021295            9 PRGFGFVTYADPSVVDKVIEDTH--II-----NGKQVEIKRTIP   45 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~~~--~i-----~g~~i~v~~~~~   45 (314)
                      .|+||||+|++.++|++|++.++  +|     .++.|.|..+..
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~  105 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK  105 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEeccc
Confidence            58999999999999999999533  33     345555555443

>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=97.15  E-value=0.00049  Score=52.40  Aligned_cols=36  Identities=17%  Similarity=0.367  Sum_probs=28.5

Q ss_pred             cEEEEEECCHHHHHHHHH--ccCccCCcE-----EEEeecCCC
Q 021295           11 GFGFVTYADPSVVDKVIE--DTHIINGKQ-----VEIKRTIPK   46 (314)
Q Consensus        11 G~aFV~f~~~~~a~~A~~--~~~~i~g~~-----i~v~~~~~~   46 (314)
                      +||||+|++.++|++||+  +..+|+++.     |+|+.+.+.
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC--
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCC
Confidence            999999999999999998  445788887     666665544

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=96.94  E-value=0.00066  Score=51.82  Aligned_cols=36  Identities=11%  Similarity=0.136  Sum_probs=31.6

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      ++||+||+|++.++|++|++  +...+.++.|.+..+.
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            69999999999999999998  4458899999998753

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=96.91  E-value=0.002  Score=49.94  Aligned_cols=37  Identities=16%  Similarity=0.227  Sum_probs=30.7

Q ss_pred             cE-EEEEECCHHHHHHHHH--ccCccCC--cEEEEeecCCCC
Q 021295           11 GF-GFVTYADPSVVDKVIE--DTHIING--KQVEIKRTIPKG   47 (314)
Q Consensus        11 G~-aFV~f~~~~~a~~A~~--~~~~i~g--~~i~v~~~~~~~   47 (314)
                      || |||+|++.++|++|++  +..+|.+  +.|.|+++.++.
T Consensus        62 Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           62 GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            86 9999999999999999  4457766  588998887664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.78  E-value=0.00051  Score=64.93  Aligned_cols=57  Identities=16%  Similarity=0.464  Sum_probs=44.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHh
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK  117 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~  117 (314)
                      ..++|+|. +|..+++.+|.++|++||+|..+.+..+.     .-||+|||.+.++++++++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            45799997 89999999999999999999999887653     35999999999999988765

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.51  E-value=0.0037  Score=45.34  Aligned_cols=35  Identities=20%  Similarity=0.329  Sum_probs=31.3

Q ss_pred             EEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCC
Q 021295           13 GFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus        13 aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~   47 (314)
                      +||+|.+.++|.+|++ +...+.++.|+|+.+.+..
T Consensus        52 ~fVtF~d~~sAlaAi~mnG~~v~Gr~LkV~lkt~dW   87 (91)
T 2dnr_A           52 MWVTFLEGSSALNVLSLNGKELLNRTITIALKSPSG   87 (91)
T ss_dssp             EEEEESSHHHHHHGGGGTTCEETTEEEEEEECCCSS
T ss_pred             EEEEECChHHHHHHHhcCCeEeCCeEEEEEeCCCCc
Confidence            8999999999999999 5568999999999987653

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.42  E-value=0.0037  Score=46.26  Aligned_cols=51  Identities=20%  Similarity=0.568  Sum_probs=43.4

Q ss_pred             cEEEEEECCHHHHHHHHHc-cCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCC
Q 021295           11 GFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVN   69 (314)
Q Consensus        11 G~aFV~f~~~~~a~~A~~~-~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~   69 (314)
                      .-|+|+|.+.+.|++.|++ .|.+.+.+|.|....++        ...+|+|.+|+..|+
T Consensus        48 ~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P~~~~--------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           48 CGGVLTFREPADAERVLAQADHELHGAQLSLRPAPPR--------APARLLLQGLPPGTS   99 (104)
T ss_dssp             TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEECCCC--------CCCCCCCCSCCCCCC
T ss_pred             CcEEEEEcChHHHHHHhcCCcceecCeEEEEEcCCCC--------CcceEeeecCCCCCC
Confidence            5689999999999999996 89999999999775543        456889999998875

>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=96.22  E-value=0.0031  Score=57.51  Aligned_cols=69  Identities=7%  Similarity=0.131  Sum_probs=40.1

Q ss_pred             cccEEEEEECCHHHHHHHHHccC--cc---CCc--EEEEeecCCCCC--CCCCCCCcceEEEcCCCCCCCHHHHHHHHhc
Q 021295            9 PRGFGFVTYADPSVVDKVIEDTH--II---NGK--QVEIKRTIPKGA--VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQ   79 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~~~--~i---~g~--~i~v~~~~~~~~--~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~   79 (314)
                      +|+||||+|++.++|++|++.++  ++   .++  .|.+........  ......+.-..|   +|..++++|=.+++++
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~~~~~~~~~~~~lp~Gl~~---~p~fis~~Ee~~Ll~~  131 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLMV---VEEIISSEEEKMLLES  131 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECSSEEEEEEECCSCCTTEEE---ETTCSCHHHHHHHHTT
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEeecccccccccccCCCceEE---EcCcCCHHHHHHHHHh
Confidence            68999999999999999999543  22   233  333333321111  011222233223   4666777777777765


Q ss_pred             c
Q 021295           80 F   80 (314)
Q Consensus        80 ~   80 (314)
                      .
T Consensus       132 i  132 (345)
T 3tht_A          132 V  132 (345)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.04  E-value=0.0067  Score=46.93  Aligned_cols=78  Identities=22%  Similarity=0.388  Sum_probs=54.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEeecC--------CCC-----CcceEEEEEeCChHHHHHHHHhcCCe
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQE-HQIMRDH--------STS-----RSRGFGFITFDTEQAVDDLLAKGNKL  121 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~-v~i~~~~--------~~g-----~~rG~afV~F~~~~~a~~a~~~l~~~  121 (314)
                      ...|.|=+.|.+.+ ..|.++|++||.|.+ +.+.++.        .+.     .......|+|+++.+|++||.+ |+.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            45677778877665 556688999999876 3222100        000     0234779999999999999999 999


Q ss_pred             eeCCeEEEEeecCC
Q 021295          122 ELAGAQVEVKKAEP  135 (314)
Q Consensus       122 ~~~gr~l~V~~a~~  135 (314)
                      .|.+.-|-|.+..+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99998777776643

>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=95.77  E-value=0.0083  Score=43.76  Aligned_cols=33  Identities=27%  Similarity=0.410  Sum_probs=29.5

Q ss_pred             EEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295           13 GFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus        13 aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      +||+|.+.++|.+||+ +...+.++.|+|+...+
T Consensus        61 ~fVtF~d~~sAl~AI~ldG~~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           61 MLVTFADSHSALSVLDVDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             EEEECSCSHHHHHHHHGGGSEETTEEEEEECCCC
T ss_pred             EEEEEcChHHHHHHHhcCCeeeCCeEEEEeccCC
Confidence            9999999999999999 66799999999987653

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.15  E-value=0.011  Score=46.76  Aligned_cols=42  Identities=10%  Similarity=0.056  Sum_probs=37.5

Q ss_pred             CCCcceEEEEEeCChHHHHHHHHhc-CCeeeCCeEEEEeecCCC
Q 021295           94 TSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        94 ~g~~rG~afV~F~~~~~a~~a~~~l-~~~~~~gr~l~V~~a~~~  136 (314)
                      ..+.+|+++|+|.++++|++|++.+ |...|++ +|.+.++..+
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            3467999999999999999999999 9999999 9999987753

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

Probab=93.54  E-value=0.041  Score=47.41  Aligned_cols=23  Identities=17%  Similarity=0.325  Sum_probs=20.7

Q ss_pred             CcccEEEEEECCHHHHHHHHHcc
Q 021295            8 QPRGFGFVTYADPSVVDKVIEDT   30 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~~   30 (314)
                      .+||||||+|.+.++|++|++.+
T Consensus       177 ~~kG~AFV~F~~~~~Ae~A~~am  199 (240)
T 3u1l_A          177 ESKNCGFVKFKYQANAEFAKEAM  199 (240)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHh
Confidence            46999999999999999999863

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.34  E-value=0.2  Score=47.95  Aligned_cols=56  Identities=16%  Similarity=0.395  Sum_probs=44.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN  119 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~  119 (314)
                      .+..++|. +|..+...+|.++|+.|+.| +|+.+.+  |     .|||.|.+++.|+.+++.++
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd--t-----~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD--T-----SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS--S-----EEEEECSCHHHHHHHHHHHT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC--C-----eEEEEECCHHHHHHHHHHHH
Confidence            34556665 99999999999999999954 4544433  2     79999999999999999864

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=88.54  E-value=0.78  Score=31.49  Aligned_cols=59  Identities=17%  Similarity=0.255  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHhccC-----CeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           67 SVNEDEFKDFFMQFG-----DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        67 ~~~e~~l~~~F~~~G-----~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .++..+|..++....     +|-.|+|..+        |.||+.... .++++++.|+...+.++.|.|+.+.
T Consensus        12 ~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~--------~s~v~v~~~-~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           12 KIRAVDFVGTIAKIDGVSADDIGIITIMDN--------ASYVEILNG-KGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             ---CHHHHHHHHTSTTCCGGGEEEEEECSS--------CEEEEECTT-CHHHHHHHHTTCCC---CCCEEECC
T ss_pred             CCCHHHHHHHHHHccCCChhhccEEEEeCC--------cEEEEECHH-HHHHHHHHhccccCcCceEEEEECC
Confidence            456677877776554     3557777654        789988654 4677888888889999999887764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.05  E-value=0.6  Score=35.55  Aligned_cols=30  Identities=13%  Similarity=0.233  Sum_probs=21.0

Q ss_pred             EEEEEECC-HHHHHHHHHccC----ccCCcEEEEe
Q 021295           12 FGFVTYAD-PSVVDKVIEDTH----IINGKQVEIK   41 (314)
Q Consensus        12 ~aFV~f~~-~~~a~~A~~~~~----~i~g~~i~v~   41 (314)
                      .|||+|.+ +++|++|+++++    .|.+..+.++
T Consensus        57 tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           57 EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            49999999 889999888532    4444444443

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=85.31  E-value=3.8  Score=29.12  Aligned_cols=69  Identities=17%  Similarity=0.150  Sum_probs=50.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC-------eeeCCeE
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-------LELAGAQ  127 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~-------~~~~gr~  127 (314)
                      +.+-|-|-|+|..+-..++.-.....|----++.+        .|.|.|.|.+.++...||.+|-+       ++|.++.
T Consensus        11 qnclikiinipqgtlkaevvlavrhlgyefycdyi--------dgqamirfqnsdeqrlaiqkllnhnnnklqieirgqi   82 (129)
T 4eyt_A           11 QNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI--------DGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIRGQI   82 (129)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC--------SSCEEEEESSHHHHHHHHHHHEETTTTEEEEEETTEE
T ss_pred             hCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee--------cCeeEEEecCChHHHHHHHHHHhcCCCEEEEEEccee
Confidence            45667889999999999988888877765555554        34799999999999999987511       3455665


Q ss_pred             EEEe
Q 021295          128 VEVK  131 (314)
Q Consensus       128 l~V~  131 (314)
                      +.|-
T Consensus        83 cdvi   86 (129)
T 4eyt_A           83 CDVI   86 (129)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            5554

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=82.48  E-value=1.2  Score=33.26  Aligned_cols=31  Identities=13%  Similarity=0.260  Sum_probs=24.8

Q ss_pred             cEEEEEECCHHHHHHHHH--ccCccCCcEEEEe
Q 021295           11 GFGFVTYADPSVVDKVIE--DTHIINGKQVEIK   41 (314)
Q Consensus        11 G~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~   41 (314)
                      +=|+|+|+|..+|-+|..  +..+|.++.|.+.
T Consensus        63 ~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           63 NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            459999999999988875  5567888887764

---

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	314
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-22
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-18
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-18
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-18
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-18
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-17
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-17
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	9e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-17
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-16
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	9e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-16
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.001
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-16
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-16
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-15
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-15
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-15
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-14
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-14
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	9e-14
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.002
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-13
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-12
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-12
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-12
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	6e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.002
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	6e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-08
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-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	6e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.002

>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 = 86.2 bits (213), Expect = 6e-22
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           KT  + V G+P    E + K++F  FG+V   Q+ +D  T  S+GFGF+ F   +    +
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 115 LAKGNKLELAGAQVEVKKAEPKK 137
           +++ + ++  G   + K    K+
Sbjct: 67  MSQRHMID--GRWCDCKLPNSKQ 87

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 2e-11
 Identities = 17/46 (36%), Positives = 25/46 (54%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 46
           KD KTG  +GFGFV + +     KV+   H+I+G+  + K    K
Sbjct: 41 KKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSK 86

>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 = 84.3 bits (208), Expect = 4e-21
 Identities = 20/96 (20%), Positives = 46/96 (47%), Gaps = 1/96 (1%)

Query: 45  PKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
           P   +  ++   + +F   + + +   + +DFF   G V++ +I+ D ++ RS+G  ++ 
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL 140
           F   Q+V   +       L G  + V+ ++ +K  L
Sbjct: 67  FCEIQSVPLAIGL-TGQRLLGVPIIVQASQAEKNRL 101

>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 = 78.4 bits (193), Expect = 4e-19
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQ 109
            K   T KI V  IP   N+ E ++ F  FG+++  ++ +  + T   RGFGF+ F T+Q
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 110 AVDDLLAK-GNKLELAGAQVEVKKAEPKK 137
                     +   L G ++ ++ A+ + 
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADSEV 91

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 2e-05
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 4/50 (8%)

Query: 1  MKDRK-TGQPRGFGFVTYADPSVVDKVIE---DTHIINGKQVEIKRTIPK 46
           K    TG  RGFGFV +       K       +  + G+++ ++    +
Sbjct: 41 PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE 90

>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 = 76.5 bits (188), Expect = 1e-18
 Identities = 26/76 (34%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+     E++ +++F  FG+V+  ++  D+ T++ RGF FITF  E+ V  ++ K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 118 GNKLELAGAQVEVKKA 133
                +  ++ E+K A
Sbjct: 61  KYH-NVGLSKCEIKVA 75

>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 = 45.3 bits (107), Expect = 3e-07
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
            D KT + RGF F+T+ +   V K++E   H +   + EIK 
Sbjct: 32 PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV 74

>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 = 77.0 bits (189), Expect = 1e-18
 Identities = 24/82 (29%), Positives = 43/82 (52%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           + ++VGG+   V++      F+ FGD+ + QI  D+ T + RGF F+ F+  +     + 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 117 KGNKLELAGAQVEVKKAEPKKP 138
             N+ EL G  + V  A+P + 
Sbjct: 66  NMNESELFGRTIRVNLAKPMRI 87

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.9 bits (193), Expect = 3e-18
 Identities = 51/140 (36%), Positives = 75/140 (53%), Gaps = 4/140 (2%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGS--KDFKTK 57
           M+D  T + RGFGFVTYA    VD  +    H ++G+ VE KR + +            K
Sbjct: 39  MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 98

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +
Sbjct: 99  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

Query: 118 GNKLELAGAQVEVKKAEPKK 137
                + G   EV+KA  K+
Sbjct: 159 KYH-TVNGHNCEVRKALSKQ 177

>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 = 56.9 bits (136), Expect = 2e-10
 Identities = 22/64 (34%), Positives = 38/64 (59%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           +K+F+GG+     ++  +  F Q+G + +  +MRD +T RSRGFGF+T+ T + VD  + 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 117 KGNK 120
               
Sbjct: 67  ARPH 70

>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 = 75.4 bits (185), Expect = 4e-18
 Identities = 26/76 (34%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+     + + KD+F +FG+V +  +  D  T RSRGFGF+ F   ++VD ++ +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 118 GNKLELAGAQVEVKKA 133
               +L G  ++ K+A
Sbjct: 61  KEH-KLNGKVIDPKRA 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 = 45.4 bits (107), Expect = 2e-07
 Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
            D  TG+ RGFGFV + +   VDKV++   H +NGK ++ KR
Sbjct: 32 KLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKR 74

>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 = 74.7 bits (183), Expect = 1e-17
 Identities = 29/96 (30%), Positives = 54/96 (56%), Gaps = 1/96 (1%)

Query: 42  RTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFG 101
            T+P      +  + +K+F+GG+     E+  ++++ Q+G + +  +MRD ++ RSRGFG
Sbjct: 6   ETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 65

Query: 102 FITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 137
           F+TF +   VD  +A      + G  VE K+A  ++
Sbjct: 66  FVTFSSMAEVDAAMAARPH-SIDGRVVEPKRAVARE 100

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK 46
          M+D  + + RGFGFVT++  + VD  +    H I+G+ VE KR + +
Sbjct: 53 MRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR 99

>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 = 73.1 bits (179), Expect = 3e-17
 Identities = 27/79 (34%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           + +K+F+GG+     ++  +  F Q+G + +  +MRD +T RSRGFGF+T+ T + VD  
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 115 LAKGNKLELAGAQVEVKKA 133
           +      ++ G  VE K+A
Sbjct: 65  M-NARPHKVDGRVVEPKRA 82

>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 = 47.0 bits (111), Expect = 9e-08
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI 44
          M+D  T + RGFGFVTYA    VD  +    H ++G+ VE KR +
Sbjct: 39 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV 83

>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 = 72.8 bits (178), Expect = 5e-17
 Identities = 24/86 (27%), Positives = 44/86 (51%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           +   ++VGG+   V+E    + F+Q G V    + +D  T + +G+GF+ F +E+  D  
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 115 LAKGNKLELAGAQVEVKKAEPKKPNL 140
           +   + ++L G  + V KA     NL
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNKNL 93

>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 = 72.3 bits (177), Expect = 6e-17
 Identities = 17/77 (22%), Positives = 32/77 (41%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            ++VG +   V E    + F   G +   ++ RD  T RS G+ ++ F      +  L  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 118 GNKLELAGAQVEVKKAE 134
            N   + G  V +  ++
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 71.6 bits (175), Expect = 1e-16
 Identities = 22/82 (26%), Positives = 46/82 (56%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+P+ +N+D+ K+    FG ++   +++D +T  S+G+ F  +      D  +A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 118 GNKLELAGAQVEVKKAEPKKPN 139
            N ++L   ++ V++A     N
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKN 84

>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 = 38.5 bits (89), Expect = 7e-05
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG 47
          +KD  TG  +G+ F  Y D +V D+ I   +   +  K++ ++R     
Sbjct: 34 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 82

>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 = 70.9 bits (173), Expect = 1e-16
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           KIFVGG+  +   ++ K +F QFG V +  +M D +T+R RGFGF+TF++E  V+ +   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 118 GNKLELAGAQVEVKKA 133
            +  E+    VE KKA
Sbjct: 61  -HFHEINNKMVECKKA 75

>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 = 38.2 bits (88), Expect = 9e-05
 Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
          M D+ T + RGFGFVT+    +V+KV E   H IN K VE K+
Sbjct: 32 MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK 74

>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 = 71.6 bits (175), Expect = 1e-16
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEH--QIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           ++F+GGIP     +E  +   +  +               ++RGF F+ +++ +A     
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 116 AK--GNKLELAGAQVEVKKAEPKK 137
            K    +++L G Q+ V  AEP+ 
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 9/50 (18%), Positives = 14/50 (28%), Gaps = 4/50 (8%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE----DTHIINGKQVEIKRTIPK 46
                 + RGF FV Y                   + G Q+ +    P+
Sbjct: 36 ASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE 85

>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 = 71.2 bits (174), Expect = 2e-16
 Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+F+GG+     ++  +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 118 GNKLELAGAQVEVKKA 133
            ++ EL    ++ K A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>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 = 70.5 bits (172), Expect = 2e-16
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
           KKIFVGGI     E   +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 117 KGNKLELAGAQVEVKKA 133
           +     + G   EV+KA
Sbjct: 63  Q-KYHTVNGHNCEVRKA 78

>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 = 40.9 bits (95), Expect = 1e-05
 Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI 44
          M DR +G+ RGF FVT+ D   VDK++    H +NG   E+++ +
Sbjct: 35 MTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL 79

>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 = 68.7 bits (167), Expect = 1e-15
 Identities = 14/78 (17%), Positives = 30/78 (38%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            +++   P S  +   +D       V     +     + SR F +I   +++     + K
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 118 GNKLELAGAQVEVKKAEP 135
            N L++ G  +  K + P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>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 = 68.1 bits (166), Expect = 2e-15
 Identities = 18/81 (22%), Positives = 35/81 (43%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
              I V  +     E + ++ F  FG +    + +D +T +S+GF FI+F   +     +
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 116 AKGNKLELAGAQVEVKKAEPK 136
           A  +        + V+ A+P 
Sbjct: 68  AGVSGFGYDHLILNVEWAKPS 88

>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 = 68.1 bits (166), Expect = 2e-15
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM---RDHSTSRSRGFGFITFDTEQAVDDLL 115
           +F+  +  S  E+  K  F + G ++   I           S GFGF+ +   +     L
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 116 AKGNKLELAGAQVEVKKAEPK-KP 138
            +     + G ++EV+ +E   KP
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>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 = 68.3 bits (166), Expect = 3e-15
 Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 8/96 (8%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQI--------MRDHSTSRSRGFGF 102
            +D     I+V G+  SV  D+  DFF Q G V+ ++           D  T + +G   
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 103 ITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP 138
           ++++        +   +  +  G++++V  A  K P
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>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 = 67.5 bits (164), Expect = 3e-15
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQ-IMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           IF+G +   ++E    D F  FG + +   IMRD  T  S+G+ FI F +  A D  +  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 118 GNKLELAGAQVEVKKAEPKKP 138
            N   L    + V  A  K  
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (165), Expect = 4e-15
 Identities = 16/94 (17%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           K+  ++VG +     E++  + F + GD+++  +  D     + GF F+ + +    ++ 
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 115 LAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRY 148
           +   N   L    +        K        R+Y
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGFKEG------RQY 93

>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 = 67.1 bits (163), Expect = 5e-15
 Identities = 28/82 (34%), Positives = 43/82 (52%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+FVGG+    NE   +  F ++G + E  +++D  T RSRGFGF+TF+      D +  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 118 GNKLELAGAQVEVKKAEPKKPN 139
            N   + G Q+ V +A     N
Sbjct: 67  MNGKSVDGRQIRVDQAGKSSDN 88

>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 = 66.2 bits (161), Expect = 1e-14
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
             K++ V  IP    + + +  F QFG + + +I+ +     S+GFGF+TF+     D  
Sbjct: 10  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRA 67

Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
             K +   + G ++EV  A  +
Sbjct: 68  REKLHGTVVEGRKIEVNNATAR 89

>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 = 65.7 bits (160), Expect = 1e-14
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 53  DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
             K   ++V  +P ++ +D+    F ++G + +  I+RD  T R RG  F+ ++  +   
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 113 DLLAKGNKLELAGA--QVEVKKA 133
           + ++  N +   G    + V+ A
Sbjct: 63  EAISALNNVIPEGGSQPLSVRLA 85

>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 = 65.5 bits (159), Expect = 2e-14
 Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           KT  + V  +P ++ ++EF+  F   G+++  +++RD  T +S G+GF+ +   +  +  
Sbjct: 2   KTN-LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 115 LAKGNKLELAGAQVEVKKAEP 135
           +   N L L    ++V  A P
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

>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 = 65.1 bits (158), Expect = 3e-14
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           S   +   ++V G+P ++ + E +  F Q+G +   +I+ D  T  SRG GFI FD    
Sbjct: 1   SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 60

Query: 111 VDDLLAKGNKLELAGA--QVEVKKA 133
            ++ +   N  + +GA   + VK A
Sbjct: 61  AEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 64.7 bits (157), Expect = 4e-14
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
             K ++V  +  S +E+  +  F         ++ +       R + F+ F   +   + 
Sbjct: 7   SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEA 60

Query: 115 LAKGNKLELAGAQVEVKKAEPKK 137
           +   N   L G+ +EV  A+P  
Sbjct: 61  MKALNGKVLDGSPIEVTLAKPVD 83

>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 = 64.4 bits (156), Expect = 9e-14
 Identities = 30/97 (30%), Positives = 45/97 (46%), Gaps = 2/97 (2%)

Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           KD    KIFVGG+P    +   + +F  FGD++E  ++ D  T +SRG+GF+T     A 
Sbjct: 6   KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 65

Query: 112 DDLLAKGNKLELAGAQVEVKKAEPK-KPNLPQPSYRR 147
           +      N   + G +  V  A    KP   Q  +  
Sbjct: 66  ERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAI 101

>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 = 64.0 bits (155), Expect = 9e-14
 Identities = 24/99 (24%), Positives = 41/99 (41%)

Query: 39  EIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSR 98
           E  R IP  +  +     K +++  +   V E +    F +F + +   I     T R R
Sbjct: 1   EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR 60

Query: 99  GFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 137
           G  FITF  ++     L   N  +L G  + ++  + KK
Sbjct: 61  GQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 99

>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 = 64.0 bits (155), Expect = 1e-13
 Identities = 24/97 (24%), Positives = 43/97 (44%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           + D   + +FVG IP    E++ KD F + G V   +++ D  T + +G+GF  +  ++ 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 111 VDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
               +   N  E +G  + V  A  +K      S   
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 8/92 (8%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
            + +++  +P  +  +E  D F ++G +++ ++        +RG  ++ ++      +  
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAC 63

Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
              +   +    + V      +      + ++
Sbjct: 64  DHLSGFNVCNRYLVVLYYNANRAFQKMDTKKK 95

>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 = 38.1 bits (88), Expect = 2e-04
 Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 14/87 (16%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKK 58
           ++   T + RG  +V Y D        +      +  + + +       A    D K K 
Sbjct: 37  IRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKK- 95

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQE 85
                      E++ K    ++G   +
Sbjct: 96  -----------EEQLKLLKEKYGINTD 111

>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 = 62.4 bits (151), Expect = 3e-13
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+++G +  +V  D+ +  F         Q++         G+ F+ +  +      +  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIET 56

Query: 118 GN-KLELAGAQVEVKKAEPKKP 138
            + K+EL G  +EV  +  KK 
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKL 78

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIED---THIINGKQVEIKRTIPKG 47
              +     G+ FV Y D +   + IE       ++GK +E+  ++ K 
Sbjct: 28 PLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK 77

>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 = 62.4 bits (151), Expect = 3e-13
 Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
              IF+  +  S++     D F  FG++   +++ D + S+   +GF+ F+T++A +  +
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAI 65

Query: 116 AKGNKLELAGAQVEVKKAEPKK 137
            K N + L   +V V + + +K
Sbjct: 66  EKMNGMLLNDRKVFVGRFKSRK 87

>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 = 62.1 bits (150), Expect = 4e-13
 Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 6/93 (6%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           S   + K +F+  +     E+   +   QFGD++  +++    T  S+G  F  F T++A
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 111 VDDLLAK------GNKLELAGAQVEVKKAEPKK 137
               LA       G  L+L G Q++V  A  + 
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 95

>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 = 61.2 bits (148), Expect = 6e-13
 Identities = 19/78 (24%), Positives = 35/78 (44%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            + V  +P  + + E    F   G +   +IMRD+ T  S G+ F+ F +E      +  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 118 GNKLELAGAQVEVKKAEP 135
            N + +   +++V  A P
Sbjct: 64  LNGITVRNKRLKVSYARP 81

>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 = 61.6 bits (149), Expect = 6e-13
 Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
             D + + ++VG +   V E      F Q G  +  +++ +H  + +  + F+ F   + 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRD 60

Query: 111 VDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
               LA  N  ++ G +V+V  A      
Sbjct: 61  AAAALAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 61.2 bits (148), Expect = 8e-13
 Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 1/82 (1%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQ-FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
              I++  +   + +DE K      F    +   +    + + RG  F+ F    +  + 
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
           L            + ++ A+  
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTD 84

>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 = 62.2 bits (150), Expect = 1e-12
 Identities = 24/118 (20%), Positives = 53/118 (44%)

Query: 33  INGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDH 92
           +   Q + ++ IP   +  +    + + V  IP++V+E + +  F ++G ++  +I+ D 
Sbjct: 19  LQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR 78

Query: 93  STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNN 150
            T +SRG+GF+ F +  +    +A  N   +   +++V  A                N
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 60.5 bits (146), Expect = 1e-12
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 55  KTKKIFVGGIPSSV-NEDEFKDFFMQFGDVQEHQIMRDH-STSRSRGFGFITFDTEQAVD 112
           + ++I +  + + + +E+  ++ F  FG +++  I       S +    F+ F+ + + +
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 113 DLLAKGNKLELAGAQVEVKKAEPK 136
             L   N+  L   ++ V  A+ K
Sbjct: 63  RALQM-NRSLLGNREISVSLADKK 85

>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 = 59.9 bits (145), Expect = 1e-12
 Identities = 14/76 (18%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           K+ V  +   V++ + ++ F +FG +++  +  D  + RS G   + F+ +      + +
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 118 GNKLELAGAQVEVKKA 133
            N + L G  + ++  
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>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 = 60.5 bits (146), Expect = 2e-12
 Identities = 21/93 (22%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 47  GAVGSK--DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
           GA GS+    +   +F+  +P    + +    FM FG+V   ++  D  T+ S+ FGF++
Sbjct: 7   GAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVS 66

Query: 105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 137
           +D   +    +   N  ++   +++V+    K 
Sbjct: 67  YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 59.6 bits (144), Expect = 4e-12
 Identities = 14/101 (13%), Positives = 29/101 (28%), Gaps = 8/101 (7%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
              +I V  +   V  D     F +FG V +           ++    + +    +    
Sbjct: 6   PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHA 61

Query: 115 LAK--GNKLELAGAQVEVKKAEPKKPNLPQ--PSYRRYNNP 151
                G  +  A   + +  ++    N+       R Y  P
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRP 102

>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 = 58.9 bits (142), Expect = 4e-12
 Identities = 19/75 (25%), Positives = 37/75 (49%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
              + V G+     E + ++ F ++G + +  I+ D  + RSRGF F+ F+      +  
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 116 AKGNKLELAGAQVEV 130
            + N +EL G ++ V
Sbjct: 69  ERANGMELDGRRIRV 83

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 6e-12
 Identities = 19/107 (17%), Positives = 43/107 (40%), Gaps = 12/107 (11%)

Query: 34  NGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS 93
           N KQ+  +  + + +      K   ++ GGI S + +   +  F  FG + E ++  +  
Sbjct: 1   NTKQLRFEDVVNQSSP-----KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG 55

Query: 94  TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL 140
                 + F+ F T ++    +   N   + G  V+    +   P++
Sbjct: 56  ------YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE-SPDM 95

>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 = 57.9 bits (139), Expect = 7e-12
 Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 3/76 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            + V  +P S N+++   +F   G +    +       ++  F  I F         + K
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAITK 59

Query: 118 GNKLELAGAQVEVKKA 133
            +K  +   ++ V   
Sbjct: 60  THK-VVGQNEIIVSHL 74

>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 = 58.2 bits (140), Expect = 9e-12
 Identities = 14/83 (16%), Positives = 33/83 (39%), Gaps = 2/83 (2%)

Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
            D K + +++ G P+    D+ K++    G V   Q+ R       +G  F+ FD+ ++ 
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESA 60

Query: 112 DDLLAKGNKLELAGAQVEVKKAE 134
              +      +     + +   +
Sbjct: 61  KKFVET-PGQKYKETDLLILFKD 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.7 bits (139), Expect = 1e-11
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 7/88 (7%)

Query: 50  GSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
           G K F  + ++FVG +P  + E+E +  F ++G   E  I +D        FGFI  +T 
Sbjct: 1   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETR 54

Query: 109 QAVDDLLAKGNKLELAGAQVEVKKAEPK 136
              +    + + + L G Q+ V+ A   
Sbjct: 55  TLAEIAKVELDNMPLRGKQLRVRFACHS 82

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 5/85 (5%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
             + +    +  ++ EDE K+ F         +I       +S+G  +I F +E   +  
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKN 69

Query: 115 LAKGNKLELAGAQVEVKKAEPKKPN 139
           L +    E+ G  V +     K   
Sbjct: 70  LEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 56.7 bits (136), Expect = 3e-11
 Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 57  KKIFVGGIPSSVNEDEFKDFFMQFGDVQE-----HQIMRDHSTSRSRGFGFITFDTEQAV 111
           ++++VG IP  + E+   DFF     +          +     ++ + F F+ F +    
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 112 DDLLAKGNKLELAGAQVEVKKAEPKKP 138
              +A  + +   G  +++++    +P
Sbjct: 62  TQAMAF-DGIIFQGQSLKIRRPHDYQP 87

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
          +   +  Q + F F+ +       + +  D  I  G+ ++I+R
Sbjct: 39 VLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR 81

>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 = 56.3 bits (135), Expect = 4e-11
 Identities = 18/85 (21%), Positives = 37/85 (43%)

Query: 52  KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
           +  +   +FV  I     EDE ++ F  +G+++   +  D  T  S+G+  + ++T +  
Sbjct: 3   RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 62

Query: 112 DDLLAKGNKLELAGAQVEVKKAEPK 136
                  N  E+ G  ++V     K
Sbjct: 63  LAAKEALNGAEIMGQTIQVDWCFVK 87

>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 = 56.4 bits (136), Expect = 4e-11
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 9/90 (10%)

Query: 56  TKKIFVGGI-PSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
             ++F+G +    V + + +  F ++G +    + +        GF F+ +  E+     
Sbjct: 15  NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAA 66

Query: 115 LAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
           +A  +   +AG  +++  A   K N   PS
Sbjct: 67  VAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>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 = 56.2 bits (135), Expect = 5e-11
 Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 7/90 (7%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           +  +FVG     + EDE ++FF Q+GDV +  I +       R F F+TF  +Q      
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQS-- 57

Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLPQPSY 145
             G  L + G  V +  AEPK  +   PS 
Sbjct: 58  LCGEDLIIKGISVHISNAEPKHNSNSGPSS 87

>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 = 39.2 bits (91), Expect = 5e-05
 Identities = 15/47 (31%), Positives = 19/47 (40%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKG 47
          M        R F FVT+AD  +   +  +  II G  V I    PK 
Sbjct: 33 MDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKH 79

>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 = 56.7 bits (136), Expect = 5e-11
 Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 3/100 (3%)

Query: 47  GAVGSK--DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
           G+ GS+         F+G +P  V E+  K+FF               +  R +GFG+  
Sbjct: 4   GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE 63

Query: 105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
           F+   ++   L+  N+  L   ++ V  A+  +     PS
Sbjct: 64  FEDLDSLLSALSL-NEESLGNKRIRVDVADQAQDKDSGPS 102

>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 = 55.9 bits (134), Expect = 9e-11
 Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 47  GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 106
           G+ GS    + ++FV  +  + +E++ +  F  +G + E     D  T + +GF F+TF 
Sbjct: 1   GSSGSSG--SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM 58

Query: 107 TEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP 138
             +      A+ +     G  + V  +  KK 
Sbjct: 59  FPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE 90

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 14/84 (16%), Positives = 30/84 (35%)

Query: 50  GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
            S       I V  +P +V+ DE  DFF  +  +     ++ +      G   + F++  
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 110 AVDDLLAKGNKLELAGAQVEVKKA 133
                +   N   +   +V++   
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVLG 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 = 35.8 bits (82), Expect = 6e-04
 Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 2/43 (4%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIK 41
          +K  + G P G   V +         + D +   I  ++V++ 
Sbjct: 42 LKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV 84

>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 = 54.9 bits (131), Expect = 2e-10
 Identities = 11/90 (12%), Positives = 26/90 (28%), Gaps = 1/90 (1%)

Query: 50  GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
           G  +       +  IP S+ + +   F       +    +   +  +  G   + F  E 
Sbjct: 2   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 110 AVDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
                    ++ +L G +  V     +   
Sbjct: 62  DARKSERL-HRKKLNGREAFVHVVTLEDMR 90

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.3 bits (124), Expect = 1e-09
 Identities = 15/87 (17%), Positives = 42/87 (48%), Gaps = 2/87 (2%)

Query: 50  GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
           GS+      +F+G +  + +  E K    +     +  ++    T  +R FG++ F++ +
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAE 65

Query: 110 AVDDLLAKGNKLELAGAQVEVKKAEPK 136
            ++  L     L++ G +++++K + +
Sbjct: 66  DLEKALEL-TGLKVFGNEIKLEKPKGR 91

>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 = 49.3 bits (117), Expect = 1e-08
 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
           K   ++V G    +     +  F  FG++ +  +             F+T++  ++ D  
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQA 55

Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
           +A+ N  ++   Q++V  A  +
Sbjct: 56  VAELNGTQVESVQLKVNIARKQ 77

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 2e-08
 Identities = 10/67 (14%), Positives = 29/67 (43%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           +++ G+     + +       +G +   + + D +T++ +G+GF+ FD+  A    +   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 119 NKLELAG 125
               +  
Sbjct: 61  KASGVQA 67

>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 = 49.1 bits (116), Expect = 3e-08
 Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 1/98 (1%)

Query: 47  GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 106
                       + + G+P   +++E   FF     V     +      RS G  F+ F 
Sbjct: 6   SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFA 65

Query: 107 TEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
           +++  +  L K +K  +    +E+ K+   +     PS
Sbjct: 66  SQEIAEKALKK-HKERIGHRYIEIFKSSRAEVRTSGPS 102

>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 = 3e-08
 Identities = 13/82 (15%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           +I+VG +P  +   + +D F ++G +++  +           F F+ F+  +  +D +  
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVYG 72

Query: 118 GNKLELAGAQVEVKKAEPKKPN 139
            +  +  G ++ V+     +  
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGT 94

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 7/79 (8%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            + V G P +         F Q+G++ +H +           +  I + ++      L+K
Sbjct: 6   WVTVFGFPQASASYILL-QFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSK 58

Query: 118 GNKLELAGAQVEVKKAEPK 136
             ++      + VK    K
Sbjct: 59  DGRIFGESIMIGVKPCIDK 77

>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 = 34.5 bits (79), Expect = 0.002
 Identities = 7/48 (14%), Positives = 13/48 (27%), Gaps = 2/48 (4%)

Query: 1  MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQ-VEIKRTIPK 46
          +          +  + Y       K +  D  I      + +K  I K
Sbjct: 30 ILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDK 77

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (112), Expect = 6e-08
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 7/90 (7%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++ V G+P S +  + KD   + GDV    + RD         G + F  ++ +   + K
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
            +  +    + E      K      PSY R
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYGR 84

>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 = 47.5 bits (112), Expect = 8e-08
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            +++  +P S++E E ++    FG       +   S+  SRG GF   ++ +  + ++  
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQ-VISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 118 GNKLELAGAQVEVKKAEP 135
            N   +          EP
Sbjct: 79  FNGKFIKTPPGVSAPTEP 96

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 10/77 (12%), Positives = 27/77 (35%), Gaps = 1/77 (1%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
               + +        E+ F +   ++G+V+E  +  +       G  ++ F  E+  +  
Sbjct: 26  AVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKA 84

Query: 115 LAKGNKLELAGAQVEVK 131
           +   N     G  +  +
Sbjct: 85  VIDLNNRWFNGQPIHAE 101

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 3e-07
 Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 13/95 (13%)

Query: 52  KDFK-----TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 106
           K+F+     +  + +  IP SV+E++ K  F   G V    +       + R    I   
Sbjct: 1   KNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMG 56

Query: 107 TEQAVDDLLAKGNKLELA-GAQVEVKKAEPKKPNL 140
           + +     L   +  +L     + V  +   K  +
Sbjct: 57  SVEEAVQALIDLHNHDLGENHHLRVSFS---KSTI 88

>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 = 44.5 bits (104), Expect = 1e-06
 Identities = 9/60 (15%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 1   MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFKTKKI 59
           +     G+  G GFV + + +     +      +  + +++     KG +   D   K++
Sbjct: 51  IAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRL 110

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 12/90 (13%), Positives = 26/90 (28%), Gaps = 7/90 (7%)

Query: 55  KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
            +  I V  +P   N  E  D    +     +          ++   F+T    +   + 
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR-------NKRTAFVTLLNGEQAQNA 56

Query: 115 LAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
           +   ++    G  + V+           PS
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>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 = 43.8 bits (103), Expect = 2e-06
 Identities = 12/91 (13%), Positives = 31/91 (34%), Gaps = 9/91 (9%)

Query: 46  KGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
           K      DF+   + +  I      ++ +    +FG +++  +   H      G   ++F
Sbjct: 14  KNMFHPMDFEDDPLVLNEI-----REDLRVECSKFGQIRKLLLFDRHP----DGVASVSF 64

Query: 106 DTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 136
              +  D  +   +     G Q+  +  +  
Sbjct: 65  RDPEEADYCIQTLDGRWFGGRQITAQAWDGT 95

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 13/106 (12%), Positives = 31/106 (29%), Gaps = 11/106 (10%)

Query: 56  TKKIFVGGIPSSVNED-----EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 110
           +  +        V  +     +F+  F  +      Q  +            I F    +
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLS 58

Query: 111 VDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYG 156
             D   + +K E  G ++++  A+         +    +   P+ G
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSSG 104

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.8 bits (97), Expect = 4e-06
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 59  IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
           I + G+P  V   E  D    +        ++     + +G  F+T    +  +  +   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 119 NKLELAGAQVEVKKA 133
           ++  L   ++ V+  
Sbjct: 54  HQSRLRERELSVQLQ 68

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.1 bits (98), Expect = 5e-06
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 55  KTKKIFVGGIPSSVNEDE---FKDFFMQFGDVQEHQIMRDHSTSRS---RGFGFITFDTE 108
           +   +FV G+   + + E     ++F +FG + +  I    S + S       ++T+   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 109 QAVDDLLAKGNKLELAGAQVEV 130
           +     +   N + + G  ++ 
Sbjct: 67  EDALRAIQCVNNVVVDGRTLKA 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.1 bits (98), Expect = 6e-06
 Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 7/88 (7%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
           ++ V G+P S +  + KD   + GDV    + +D         G + +  ++ ++  L K
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDMEYALRK 69

Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPSY 145
            +  +    + E             PS 
Sbjct: 70  LDDTKFRSHEGETSYIRVYPERSSGPSS 97

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 8/91 (8%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           +  + V G+  SV E +  +   +FG +    +M             + F+   +  + +
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECV 68

Query: 116 AK--GNKLELAGAQVEVKKAEPKKPNLPQPS 144
                  + +AG Q     +  K+   P  S
Sbjct: 69  TFAADVPVYIAGQQAFFNYSTSKRITRPGNS 99

>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 = 41.1 bits (95), Expect = 2e-05
 Identities = 21/117 (17%), Positives = 36/117 (30%), Gaps = 13/117 (11%)

Query: 47  GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF- 105
           G+ GS       I    +P+     E ++ F +FG +    +              + F 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFL 54

Query: 106 ---DTEQAVDDL---LAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYG 156
              +  +A   L         L L  A + V  A P+K +             P+ G
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSSG 111

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 2e-05
 Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 12/85 (14%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAV 111
           ++ + +  +P  V E E     + FG V    +++  +        F+           V
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------QAFLELATEEAAITMV 61

Query: 112 DDLLAKGNKLELAGAQVEVKKAEPK 136
           +          L    + ++ +  K
Sbjct: 62  NYY--SAVTPHLRNQPIYIQYSNHK 84

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 12/82 (14%), Positives = 22/82 (26%), Gaps = 7/82 (8%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-QAVDDL 114
               F G +      ++    F   G+++    +R          G I F  + +     
Sbjct: 11  CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGK 64

Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
               N   L     EV     +
Sbjct: 65  AKDANNGNLQLRNKEVTWEVLE 86

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 6e-05
 Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 58  KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
            + + G+P    E++  +FF     ++ H  +      R  G   + F T +     +AK
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFATHEDAVAAMAK 74

Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
            +K  +    VE+        +   PS
Sbjct: 75  -DKANMQHRYVELFLNSTAGTSGSGPS 100

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 37.5 bits (86), Expect = 2e-04
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
            + +F+  +P   NE      F QF   +E +++ +          F+ F TE   +   
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAK 62

Query: 116 AKGNKLEL-AGAQVEVKKAEPKK 137
                 ++     +++  A  KK
Sbjct: 63  EALQGFKITPTHAMKITFA--KK 83

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 56  TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
           T +++VGG+  + +       F +FG ++    ++  S      F +I +++  A     
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAAC 70

Query: 116 AKGNKLELAGA--QVEVKKAEPKK 137
           AK     L G   ++ V  A+   
Sbjct: 71  AKMRGFPLGGPDRRLRVDFAKSGP 94

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 10/68 (14%)

Query: 51  SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT--- 107
           S   ++  +  GG+ + V+ ++      + G V    +  +        + F  + T   
Sbjct: 15  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEE 68

Query: 108 -EQAVDDL 114
            ++A   L
Sbjct: 69  SKRAYVTL 76

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 2/70 (2%)

Query: 70  EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF--ITFDTEQAVDDLLAKGNKLELAGAQ 127
            ++ +D   ++G V+  +I R        G G   + F +       +      + A   
Sbjct: 28  VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 87

Query: 128 VEVKKAEPKK 137
           V  K  +P  
Sbjct: 88  VVTKYCDPDS 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	314
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.92
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.87
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.87
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.87
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.85
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.84
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.83
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.81
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.8
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.78
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.78
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.78
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.77
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.76
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.75
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.75
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.74
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.7
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.68
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	99.6
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.54
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.53
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.52
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.45
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.41
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.72
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.67
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.67
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.66
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.65
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.64
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.63
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.62
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.61
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.6
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.6
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.59
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.58
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.58
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.56
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.53
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.52
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	98.52
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.52
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.49
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.48
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.47
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	98.47
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	98.46
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.45
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.45
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.44
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.43
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.43
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.42
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.4
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.39
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.39
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.34
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.32
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.32
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.3
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	98.3
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.28
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.26
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.25
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.22
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.22
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.22
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.2
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.18
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.18
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.16
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.16
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.12
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.11
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.11
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.1
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.07
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.05
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	98.01
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.01
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.01
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.0
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	97.97
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.95
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.94
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	97.92
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.89
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	97.87
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	97.84
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	97.82
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	97.78
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	97.78
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.7
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	97.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.61
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	97.6
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	97.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	97.58
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.57
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	97.54
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	97.46
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	97.45
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.36
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	97.27
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	97.27
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	97.18
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	97.16
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.9
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.69
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	96.13
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.33
d2od6a1	109	Hypothetical protein GOS_2359375 {environmental sa	85.31

>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=99.92  E-value=8.9e-25  Score=182.13  Aligned_cols=137  Identities=37%  Similarity=0.690  Sum_probs=120.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC--CCCCCcceEEEcCCCCCCCHHHHHHHH
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG--SKDFKTKKIFVGGIPSSVNEDEFKDFF   77 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~--~~~~~~~~l~V~nLp~~~~e~~l~~~F   77 (314)
                      |+|+.|+++++||||+|.+.++|++|+. ....+..+.+.+++..+.....  ......++|||.|||+++++++|+++|
T Consensus        39 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f  118 (183)
T d1u1qa_          39 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF  118 (183)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHH
T ss_pred             eecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhh
Confidence            3578899999999999999999999999 4446778888887766554332  355677899999999999999999999


Q ss_pred             hccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCCC
Q 021295           78 MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP  138 (314)
Q Consensus        78 ~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~~  138 (314)
                      ++||+|+.|.|+.++.++++++||||+|+++++|++||+ ++...|++++|+|++|.+++.
T Consensus       119 ~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         119 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQE  178 (183)
T ss_dssp             GGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHHH
T ss_pred             ccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCccc
Confidence            999999999999999999999999999999999999997 588899999999999987643

>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=99.88  E-value=2.8e-22  Score=150.40  Aligned_cols=86  Identities=21%  Similarity=0.361  Sum_probs=81.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ..+++|||+|||++++|+||+++|++|++|++|+|++|+.++++++||||+|+++++|++||+.||+..|.+++|+|++|
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 021295          134 EPKKPN  139 (314)
Q Consensus       134 ~~~~~~  139 (314)
                      .+++..
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            987543

>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=99.87  E-value=1.9e-22  Score=149.53  Aligned_cols=85  Identities=26%  Similarity=0.503  Sum_probs=81.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++|+.++++++||||+|.++++|++||+.||+..|.+++|+|++|
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            34579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      .++..
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            98764

>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=99.87  E-value=1.4e-22  Score=149.10  Aligned_cols=84  Identities=29%  Similarity=0.571  Sum_probs=80.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ..++|||+|||++++|++|+++|++||+|++|+|+.|+.+++++|||||+|+++++|++||+.||+..|.+++|+|++|.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      +++.
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.87  E-value=2.4e-22  Score=147.49  Aligned_cols=84  Identities=21%  Similarity=0.371  Sum_probs=79.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..+..+|||.|||+++++++|+++|++||+|++|+|++|+.++++++||||+|++.++|++|++.||+..|.+++|+|++
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            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 021295          133 AEPK  136 (314)
Q Consensus       133 a~~~  136 (314)
                      |.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9865

>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=99.87  E-value=4.9e-22  Score=158.38  Aligned_cols=88  Identities=23%  Similarity=0.479  Sum_probs=81.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +....++|||+|||++++|++|+++|++||+|++|+|++|+.|+++++||||+|++.++|++||+.||++.|.+++|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33455789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      +|.++...
T Consensus       118 ~a~~~~~~  125 (139)
T d1u6fa1         118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             EcCCCCCC
Confidence            99876543

>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=99.87  E-value=7.9e-22  Score=146.18  Aligned_cols=84  Identities=17%  Similarity=0.283  Sum_probs=80.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .++++|||+|||+++||++|+++|++||+|++|.|++++.++++++||||+|+++++|++||+.||+..|++++|+|++|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 021295          134 EPKK  137 (314)
Q Consensus       134 ~~~~  137 (314)
                      ...+
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.87  E-value=3.7e-22  Score=147.12  Aligned_cols=85  Identities=21%  Similarity=0.409  Sum_probs=80.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ..++++|||.|||.+++|++|+++|++||+|++|+|++|+.++++++||||+|++.++|++||+.||+..|.+++|+|++
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            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 021295          133 AEPKK  137 (314)
Q Consensus       133 a~~~~  137 (314)
                      |+++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98764

>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=99.87  E-value=2.5e-22  Score=145.42  Aligned_cols=80  Identities=24%  Similarity=0.457  Sum_probs=77.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      .++|||+|||++++|++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|.+++|+|++|+|
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            46799999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.87  E-value=6.9e-22  Score=149.03  Aligned_cols=86  Identities=20%  Similarity=0.451  Sum_probs=81.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      .++.++|||.|||++++|++|+++|++||+|++|.|+.++.++++||||||+|+++++|++||+.||+..|.+++|+|++
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      |.++..
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            988764

>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=99.87  E-value=9.2e-22  Score=144.79  Aligned_cols=84  Identities=27%  Similarity=0.507  Sum_probs=77.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEee
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK  132 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~  132 (314)
                      ...+++|||+|||+++||++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||+.+  ..|+++.|.|++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEe
Confidence            345688999999999999999999999999999999999999999999999999999999999864  479999999999


Q ss_pred             cCCCCC
Q 021295          133 AEPKKP  138 (314)
Q Consensus       133 a~~~~~  138 (314)
                      |.+++.
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            988654

>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=99.86  E-value=7e-22  Score=142.99  Aligned_cols=79  Identities=24%  Similarity=0.554  Sum_probs=76.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ++|||+|||++++|++|+++|++||+|++|+|+++..++++++||||+|+++++|++|++.||+..|.+++|+|++|+|
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.86  E-value=1.1e-21  Score=148.09  Aligned_cols=85  Identities=32%  Similarity=0.591  Sum_probs=78.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ++...++|||+|||++++|+||+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.+|. .|.+++|+|+
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            444567899999999999999999999999999999999999999999999999999999999999876 7999999999


Q ss_pred             ecCCCC
Q 021295          132 KAEPKK  137 (314)
Q Consensus       132 ~a~~~~  137 (314)
                      +|..+.
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            988654

>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=99.86  E-value=8.4e-22  Score=141.91  Aligned_cols=77  Identities=22%  Similarity=0.382  Sum_probs=75.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +|||+|||+++||++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+..|.+++|+|++|+
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            69999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.86  E-value=5.5e-22  Score=144.53  Aligned_cols=81  Identities=26%  Similarity=0.576  Sum_probs=78.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      .+|||+|||+++||++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++|++.||+..|.+++|.|++|.+.
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            47999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             C
Q 021295          137 K  137 (314)
Q Consensus       137 ~  137 (314)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.6e-21  Score=141.43  Aligned_cols=78  Identities=24%  Similarity=0.475  Sum_probs=74.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ..++++|||+|||+++||++|+++|++||+|++|+|+.++.++++++||||+|+++++|++||++||+..|.+++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.86  E-value=1.1e-21  Score=143.02  Aligned_cols=81  Identities=22%  Similarity=0.566  Sum_probs=76.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEV  130 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V  130 (314)
                      +.+.++|||+|||++++|++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+..+.+  ++|+|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            3456789999999999999999999999999999999999999999999999999999999999999999876  88999


Q ss_pred             eec
Q 021295          131 KKA  133 (314)
Q Consensus       131 ~~a  133 (314)
                      ++|
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            986

>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=99.85  E-value=9.1e-22  Score=148.46  Aligned_cols=83  Identities=33%  Similarity=0.688  Sum_probs=78.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||+|||++++|++|+++|++||+|+.|.|++|+.+.++++||||+|++.++|++||+ ++...|+++.|.|++|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            45799999999999999999999999999999999999999999999999999999999996 58889999999999999


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      +++.
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            8764

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.6e-21  Score=140.58  Aligned_cols=80  Identities=34%  Similarity=0.649  Sum_probs=75.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||++++|++|+++|++||+|++|+|+.|+.+++++|||||+|.++++|++||+. +...|.++.|+|+.|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCCEECCEEEEEEee
Confidence            3568999999999999999999999999999999999999999999999999999999999985 888999999999988


Q ss_pred             C
Q 021295          134 E  134 (314)
Q Consensus       134 ~  134 (314)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.85  E-value=1.2e-21  Score=144.36  Aligned_cols=85  Identities=33%  Similarity=0.629  Sum_probs=80.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||+|||++++|++|+++|++||+|+.|.++.+..++++++||||+|+++++|++||+.||+..|.+++|+|++|.
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            56789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 021295          135 PKKPN  139 (314)
Q Consensus       135 ~~~~~  139 (314)
                      ++...
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.85  E-value=1.7e-21  Score=141.89  Aligned_cols=80  Identities=29%  Similarity=0.583  Sum_probs=75.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEEEe
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVEVK  131 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~V~  131 (314)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++|+.++++++||||+|+++++|++|++.||+..+.+  ++|+|+
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            345789999999999999999999999999999999999999999999999999999999999999999987  569998


Q ss_pred             ec
Q 021295          132 KA  133 (314)
Q Consensus       132 ~a  133 (314)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.85  E-value=7.5e-22  Score=148.43  Aligned_cols=82  Identities=21%  Similarity=0.439  Sum_probs=77.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||++++|++|+++|++||+|++|+|++|+.++++||||||+|+++++|++||+ ||+..|.+++|.|++|
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            346799999999999999999999999999999999999999999999999999999999996 8999999999999988


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      .++
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>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=99.84  E-value=8.3e-22  Score=149.16  Aligned_cols=83  Identities=27%  Similarity=0.564  Sum_probs=79.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||+|||++++|++|+++|++||+|++|+|++++.++++++||||+|++.++|++||+.||+..|.+++|+|++|.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCC
Q 021295          135 PKK  137 (314)
Q Consensus       135 ~~~  137 (314)
                      +++
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=4.3e-21  Score=142.45  Aligned_cols=86  Identities=27%  Similarity=0.484  Sum_probs=79.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCC-CCCcceEEEEEeCChHHHHHHHHhc-CCeeeCCeEEEE
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQVEV  130 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~-~g~~rG~afV~F~~~~~a~~a~~~l-~~~~~~gr~l~V  130 (314)
                      ..++++|||.|||++++|++|+++|++||+|++|+|++++. ++++++||||+|+++++|++||+.| |...|.+++|.|
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            34568899999999999999999999999999999998854 7899999999999999999999998 889999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      ++|.++..
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987653

>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=99.84  E-value=2.6e-21  Score=140.25  Aligned_cols=80  Identities=31%  Similarity=0.497  Sum_probs=75.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEE-EEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCCC
Q 021295           59 IFVGGIPSSVNEDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  137 (314)
Q Consensus        59 l~V~nLp~~~~e~~l~~~F~~~G~v~~-v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~~  137 (314)
                      |||+|||++++|++|+++|++||+|++ +.|++++.++++++||||+|+++++|++||+.||+..|.+++|+|++|.+++
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            899999999999999999999999876 4789999999999999999999999999999999999999999999998765


Q ss_pred             C
Q 021295          138 P  138 (314)
Q Consensus       138 ~  138 (314)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1e-20  Score=140.04  Aligned_cols=85  Identities=26%  Similarity=0.499  Sum_probs=78.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .....++|||+|||+++++++|+++|++||+|++|+|+.++.+  +++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4556788999999999999999999999999999999988644  78999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      +|+++..
T Consensus        85 ~A~~r~~   91 (93)
T d2cq3a1          85 NATARVM   91 (93)
T ss_dssp             ECCSSCC
T ss_pred             ecCcCCC
Confidence            9998654

>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=2.2e-21  Score=137.91  Aligned_cols=75  Identities=35%  Similarity=0.733  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +|||+|||++++|++|+++|++||+|+.|+|++|+.++++++||||+|+++++|++||+ ++...|+++.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999998 5888999999999765

>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=99.84  E-value=5.4e-21  Score=139.21  Aligned_cols=78  Identities=22%  Similarity=0.456  Sum_probs=73.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCC---CcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        59 l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g---~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      |||+|||+++|+++|+++|++||+|++|.|++++.+.   ++||||||+|+++++|++|++.||+..|.+++|+|++|.+
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            8999999999999999999999999999999987665   4689999999999999999999999999999999999865


Q ss_pred             C
Q 021295          136 K  136 (314)
Q Consensus       136 ~  136 (314)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.84  E-value=4.8e-21  Score=137.16  Aligned_cols=77  Identities=18%  Similarity=0.404  Sum_probs=73.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      +|||+|||++++|++|+++|++||+|++|+|+.++ ++++++||||+|+++++|++|++.||+..|.+++|+|++|..
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999985 889999999999999999999999999999999999999863

>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=1.3e-20  Score=138.70  Aligned_cols=84  Identities=21%  Similarity=0.400  Sum_probs=76.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ++.+.++|||+|||.+++|++|+++|++||+|++|+|+.++.+.  ++||||+|++.++|++|++.||+..|.+++|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34557899999999999999999999999999999999987654  7899999999999999999999999999999999


Q ss_pred             ecCCCC
Q 021295          132 KAEPKK  137 (314)
Q Consensus       132 ~a~~~~  137 (314)
                      +|.++.
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            998653

>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=99.84  E-value=1.3e-21  Score=139.80  Aligned_cols=76  Identities=41%  Similarity=0.747  Sum_probs=72.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ++|||+|||+++||++|+++|++||+|++|+|++|+.|+++||||||+|+++++|++||+ ++...|++++|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            479999999999999999999999999999999999999999999999999999999998 4999999999999876

>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=99.84  E-value=3.3e-21  Score=139.03  Aligned_cols=79  Identities=18%  Similarity=0.305  Sum_probs=69.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ++|||+|||+++||++|+++|++||+|+.+.++.+..++++++||||+|+++++|++||+.||+..|.+++|.|++++|
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            6899999999999999999999999999999998888999999999999999999999999999999999999999986

>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=1.4e-20  Score=135.08  Aligned_cols=77  Identities=39%  Similarity=0.760  Sum_probs=73.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .++|||+|||+++||++|+++|++||+|+.+.++.++.++++++||||+|++++++++|++ +++..|.+++|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            5799999999999999999999999999999999999999999999999999999999996 6999999999999877

>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=99.83  E-value=1.6e-20  Score=140.37  Aligned_cols=87  Identities=25%  Similarity=0.429  Sum_probs=79.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcC------CeeeCC
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN------KLELAG  125 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~------~~~~~g  125 (314)
                      ...+.++|||+|||+++||++|+++|++||+|+++.++.++.+.++++||||+|.++++|++||+.||      +..|.+
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            34456899999999999999999999999999999999999999999999999999999999999875      678999


Q ss_pred             eEEEEeecCCCCC
Q 021295          126 AQVEVKKAEPKKP  138 (314)
Q Consensus       126 r~l~V~~a~~~~~  138 (314)
                      ++|+|++|.++.+
T Consensus        84 r~l~v~~a~~k~~   96 (98)
T d1x4ha1          84 RQLKVDLAVTRDE   96 (98)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCCc
Confidence            9999999987643

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.5e-21  Score=137.48  Aligned_cols=75  Identities=35%  Similarity=0.676  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +|||+|||+++||++|+++|++||+|++|+|++|+.+++++|||||+|+++++|++||+. +...|.++.|+|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999986 667899999999875

>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=99.83  E-value=1.3e-20  Score=141.71  Aligned_cols=88  Identities=25%  Similarity=0.416  Sum_probs=80.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~--------~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      ++.+.++|||+|||++++|++|+++|++||+|+        .+.++.++.++++++||||+|+++++|++||+.||++.|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            455678999999999999999999999999874        577888888999999999999999999999999999999


Q ss_pred             CCeEEEEeecCCCCCC
Q 021295          124 AGAQVEVKKAEPKKPN  139 (314)
Q Consensus       124 ~gr~l~V~~a~~~~~~  139 (314)
                      .+++|+|++|+++.+.
T Consensus        84 ~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          84 QGSKLKVSLARKKPPM   99 (101)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCEEEEEEEcCCCCCC
Confidence            9999999999876543

>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=99.83  E-value=1e-20  Score=138.93  Aligned_cols=81  Identities=26%  Similarity=0.530  Sum_probs=75.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  135 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~  135 (314)
                      ..+|||+|||+++++++|+++|++||+|++++|+.++.+  +++||||+|+++++|++||+.||+..|.+++|.|++|++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~--~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB--CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            457999999999999999999999999999999998643  789999999999999999999999999999999999987


Q ss_pred             CCC
Q 021295          136 KKP  138 (314)
Q Consensus       136 ~~~  138 (314)
                      +++
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            653

>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=99.82  E-value=2e-20  Score=136.43  Aligned_cols=82  Identities=18%  Similarity=0.375  Sum_probs=71.8

Q ss_pred             CCcceEEEcCCCCCCC-HHHHHHHHhccCCeEEEEEeec-CCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           54 FKTKKIFVGGIPSSVN-EDEFKDFFMQFGDVQEHQIMRD-HSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~-e~~l~~~F~~~G~v~~v~i~~~-~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+.++|||.|||++++ |++|+++|++||+|++|+|+.+ ..+++++|||||+|++.++|++||+ ||+..|.+++|+|+
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            3578999999999875 6679999999999999998764 5688999999999999999999996 89999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      +|+++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99875

>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=1.8e-20  Score=133.02  Aligned_cols=75  Identities=41%  Similarity=0.729  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        58 ~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +|||+|||+++||++|+++|++||.|+.+.++.++.++++++||||+|+++++|++||+ +|+..|++++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 8999999999999876

>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=99.81  E-value=7.5e-21  Score=143.25  Aligned_cols=87  Identities=23%  Similarity=0.313  Sum_probs=81.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...++++|||.|||.++++++|+++|++||.|+.+.|+.+..++++++||||+|.++++|++||+.||+..|.+++|+|+
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 021295          132 KAEPKKP  138 (314)
Q Consensus       132 ~a~~~~~  138 (314)
                      +|++++.
T Consensus        94 ~ak~k~~  100 (102)
T d2cpxa1          94 FGKNKKQ  100 (102)
T ss_dssp             ECCCCSC
T ss_pred             eCCCccc
Confidence            9998754

>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=99.80  E-value=1.2e-20  Score=139.02  Aligned_cols=83  Identities=16%  Similarity=0.362  Sum_probs=75.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ++....+|||+|||++++|++|+++|++||+|+.++|+.+ .++++++||||+|+++++|++||+ ||+..|.+++|+|+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3445679999999999999999999999999999888755 688999999999999999999996 89999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      +|+.+
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            98864

>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=99.80  E-value=1.3e-19  Score=136.78  Aligned_cols=85  Identities=22%  Similarity=0.458  Sum_probs=74.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecC-CCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~-~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      +.++++|||.|||++++|++|+++|++|+ |+++.|+.+. .++++++||||+|+++++|++|+ +||++.|.+++|+|+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            34568999999999999999999999998 7777777665 47889999999999999998776 589999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      +|.+++..
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99877554

>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=1.9e-19  Score=135.97  Aligned_cols=88  Identities=17%  Similarity=0.269  Sum_probs=78.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+..+|||.|||+++||+||+++|+.++.|+.+.++.+..+++++|||||+|+++++|++||+ +|...|.+|.|+|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34456689999999999999999999999999887777777889999999999999999999996 69999999999999


Q ss_pred             ecCCCCCCC
Q 021295          132 KAEPKKPNL  140 (314)
Q Consensus       132 ~a~~~~~~~  140 (314)
                      ++.+++...
T Consensus        90 ~~~~~~~~~   98 (104)
T d1wg5a_          90 KSSRAEVRT   98 (104)
T ss_dssp             EECTTTSCC
T ss_pred             ECCHHHhcc
Confidence            998876544

>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=99.80  E-value=1.6e-19  Score=134.76  Aligned_cols=79  Identities=18%  Similarity=0.421  Sum_probs=70.5

Q ss_pred             CCCCcceEEEcCCC-CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           52 KDFKTKKIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        52 ~~~~~~~l~V~nLp-~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ......+|||+||| +.++|+||+++|++||+|++|+|.        |+||||+|+++++|++||+.||+.+|.+++|+|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34455789999996 578899999999999999999983        689999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      +++.+++.
T Consensus        83 ~~a~~~~~   90 (98)
T d1wf2a_          83 NLAAEPKV   90 (98)
T ss_dssp             EETTSCCC
T ss_pred             EECCCCCC
Confidence            99986543

>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=99.79  E-value=2.4e-19  Score=133.09  Aligned_cols=80  Identities=16%  Similarity=0.461  Sum_probs=72.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||++++++||+++|++|+.|+.|.+..+   ..+++||||+|+++++|++||+.||++.|.+++|+|++|
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            45578999999999999999999999999999988654   346899999999999999999999999999999999998


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=99.79  E-value=2e-19  Score=133.71  Aligned_cols=78  Identities=21%  Similarity=0.461  Sum_probs=72.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||.+++|++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.||+..|.+++|+|+|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999976      679999999999999999999999999999999999


Q ss_pred             CCCC
Q 021295          134 EPKK  137 (314)
Q Consensus       134 ~~~~  137 (314)
                      +++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.8e-19  Score=129.93  Aligned_cols=79  Identities=16%  Similarity=0.353  Sum_probs=73.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||+|||+++|+++|+++|++||+|+.|+|+.++ +++++|||||+|+++++|++||+ ++++.|.+++|.|+++.
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 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            46799999999999999999999999999999998874 88999999999999999999996 59999999999999865


Q ss_pred             C
Q 021295          135 P  135 (314)
Q Consensus       135 ~  135 (314)
                      +
T Consensus        83 d   83 (85)
T d1zh5a2          83 D   83 (85)
T ss_dssp             G
T ss_pred             C
Confidence            4

>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=99.79  E-value=9.6e-20  Score=136.85  Aligned_cols=83  Identities=23%  Similarity=0.487  Sum_probs=76.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      .+.++++|||+|||++++|++|+++|++||+|+.+.++.+ .+.++++||||+|+++++|++||+.||+..|.+++|.|.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            3445689999999999999999999999999999999988 478899999999999999999999999999999999887


Q ss_pred             ecCC
Q 021295          132 KAEP  135 (314)
Q Consensus       132 ~a~~  135 (314)
                      ++.|
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7665

>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=99.78  E-value=3.1e-19  Score=132.75  Aligned_cols=84  Identities=19%  Similarity=0.339  Sum_probs=74.5

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        50 ~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      .....+.++|||+|||++++|+||+++|++||+|..+.     .++++++||||+|++.++|++||+.||+..|.+++|+
T Consensus        10 ~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~   84 (96)
T d1fjca_          10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             cCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEE
Confidence            33455678999999999999999999999999876554     2567899999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q 021295          130 VKKAEPKKP  138 (314)
Q Consensus       130 V~~a~~~~~  138 (314)
                      |.++.++..
T Consensus        85 V~~a~~k~~   93 (96)
T d1fjca_          85 LYYTGEKGG   93 (96)
T ss_dssp             EEECSSSCC
T ss_pred             EEEeCCCCC
Confidence            999998754

>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=99.78  E-value=1.7e-19  Score=131.41  Aligned_cols=80  Identities=16%  Similarity=0.258  Sum_probs=71.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +...+|||.|||++++|+||+++|+.|+.|....++.+..+++++++|||+|+++++|++||++||+..|.+++|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44568999999999999999999999999876444444478999999999999999999999999999999999999875

>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=99.78  E-value=3.4e-19  Score=132.51  Aligned_cols=84  Identities=24%  Similarity=0.421  Sum_probs=75.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEeecC-CCCCcceEEEEEeCChHHHHHHHHhcC--CeeeCCeEEEEee
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGD-VQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVEVKK  132 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~-v~~v~i~~~~-~~g~~rG~afV~F~~~~~a~~a~~~l~--~~~~~gr~l~V~~  132 (314)
                      ++|||+|||.+++|++|+++|++||+ |+.|.|+++. .++++++||||+|+++++|++|++.|+  .+.+.+++|.|++
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            57999999999999999999999996 8999999885 468899999999999999999999985  4566899999999


Q ss_pred             cCCCCCCC
Q 021295          133 AEPKKPNL  140 (314)
Q Consensus       133 a~~~~~~~  140 (314)
                      |++++...
T Consensus        82 A~p~~~~~   89 (96)
T d2disa1          82 AEPEIDVD   89 (96)
T ss_dssp             SCSSCSTT
T ss_pred             cCCCCCCC
Confidence            98876543

>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=99.78  E-value=1.3e-19  Score=132.69  Aligned_cols=79  Identities=34%  Similarity=0.622  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ..+++|||+|||+++||+||+++|++||+|++|+++.+     +++||||+|+++++|++||+  +.+.|++++|.|++|
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            35789999999999999999999999999999987543     57899999999999999986  678899999999999


Q ss_pred             CCCCCC
Q 021295          134 EPKKPN  139 (314)
Q Consensus       134 ~~~~~~  139 (314)
                      .++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.78  E-value=5.3e-19  Score=135.66  Aligned_cols=80  Identities=10%  Similarity=0.299  Sum_probs=73.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ..+++|||+|||+++++++|+++|++||+|++|+|..+   .+++|||||+|++.++|++||+.||+..|.+++|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34679999999999999999999999999999999865   456899999999999999999999999999999999998


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      .+.
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            654

>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=99.78  E-value=3.8e-19  Score=128.68  Aligned_cols=79  Identities=16%  Similarity=0.315  Sum_probs=71.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeC-CeEEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQVE  129 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~-gr~l~  129 (314)
                      .+.+++++|||.|||.++++++|+++|++||+|++|+|+++     .++||||+|++.++|++|++.||+..|. +++|+
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEE
Confidence            34566789999999999999999999999999999999865     3679999999999999999999998884 68999


Q ss_pred             EeecC
Q 021295          130 VKKAE  134 (314)
Q Consensus       130 V~~a~  134 (314)
                      |++|+
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99986

>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=99.78  E-value=1.2e-18  Score=126.90  Aligned_cols=79  Identities=19%  Similarity=0.302  Sum_probs=71.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||+|||++++|++|+++|++|+.|+.+.+..      +++||||+|.++++|++||+.||+..|.+++|+|++|
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3468999999999999999999999999998887754      4779999999999999999999999999999999999


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      +|+..
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87643

>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=99.78  E-value=3.8e-19  Score=133.79  Aligned_cols=85  Identities=16%  Similarity=0.232  Sum_probs=74.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ......+|||.|||+++||+||+++|+.++ |+.|.|+.+. ++++++||||+|+++++|++||+ ||+..|.+|.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            445667999999999999999999999997 5578888874 57899999999999999999986 69999999999999


Q ss_pred             ecCCCCCC
Q 021295          132 KAEPKKPN  139 (314)
Q Consensus       132 ~a~~~~~~  139 (314)
                      ++.+....
T Consensus        88 ~s~~~~~~   95 (102)
T d1weza_          88 LNSTAGTS   95 (102)
T ss_dssp             EECCCCCC
T ss_pred             EcCCCCCC
Confidence            98876543

>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=99.78  E-value=2.2e-19  Score=131.67  Aligned_cols=79  Identities=16%  Similarity=0.320  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHH---HHHHhccCCeEEEEEeecCCCCCc---ceEEEEEeCChHHHHHHHHhcCCeeeCCe
Q 021295           53 DFKTKKIFVGGIPSSVNEDEF---KDFFMQFGDVQEHQIMRDHSTSRS---RGFGFITFDTEQAVDDLLAKGNKLELAGA  126 (314)
Q Consensus        53 ~~~~~~l~V~nLp~~~~e~~l---~~~F~~~G~v~~v~i~~~~~~g~~---rG~afV~F~~~~~a~~a~~~l~~~~~~gr  126 (314)
                      ..+.++|||.|||++++++||   +++|++||+|++|.|++++.+..+   ++||||+|+++++|++||+.||+..|.++
T Consensus         5 viq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr   84 (89)
T d2cpia1           5 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   84 (89)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             EEecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCE
Confidence            345678999999999999999   678999999999999999877654   49999999999999999999999999999


Q ss_pred             EEEEe
Q 021295          127 QVEVK  131 (314)
Q Consensus       127 ~l~V~  131 (314)
                      +|+|+
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99985

>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=99.77  E-value=4.1e-19  Score=129.35  Aligned_cols=77  Identities=29%  Similarity=0.590  Sum_probs=71.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ..++|||+|||+++++++|+++|++||+|++|+|+++      ++||||+|++.++|++|++.||+..|.+++|+|++|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3567999999999999999999999999999999865      5799999999999999999999999999999999998


Q ss_pred             CCC
Q 021295          135 PKK  137 (314)
Q Consensus       135 ~~~  137 (314)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            764

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=5.8e-19  Score=134.32  Aligned_cols=78  Identities=14%  Similarity=0.262  Sum_probs=71.5

Q ss_pred             cceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           56 TKKIFVGGIPS-SVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        56 ~~~l~V~nLp~-~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +++|||.|||+ .++|++|+++|++||+|++|.|++++     ++||||+|+++++|++||+.||+..|.+++|+|++++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            47899999955 69999999999999999999999873     7899999999999999999999999999999999987


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      ....
T Consensus        77 ~~~~   80 (109)
T d2adca1          77 HQNV   80 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>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=99.77  E-value=2.6e-19  Score=128.62  Aligned_cols=76  Identities=20%  Similarity=0.378  Sum_probs=69.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC-eeeCCeEEEEeecCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-LELAGAQVEVKKAEP  135 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~-~~~~gr~l~V~~a~~  135 (314)
                      ++|||+|||++++|++|+++|++||.|..+.++..      ++||||+|+++++|++|++.||+ +.|.+++|+|++|.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            57999999999999999999999999988777654      67999999999999999999997 579999999999998


Q ss_pred             CCC
Q 021295          136 KKP  138 (314)
Q Consensus       136 ~~~  138 (314)
                      ++.
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            764

>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=9.9e-20  Score=132.99  Aligned_cols=74  Identities=23%  Similarity=0.357  Sum_probs=68.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      ++|||+|||+++++++|+++|++||+|++|+|+.+       +||||+|++.++|++||++||+.+|.++.|+|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999999999999999998754       69999999999999999999999999999999887655


Q ss_pred             C
Q 021295          137 K  137 (314)
Q Consensus       137 ~  137 (314)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            4

>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=127.06  Aligned_cols=78  Identities=14%  Similarity=0.250  Sum_probs=67.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      .+++|||.|||++++++||+++|++|| |+.+.+.      ++++||||+|+++++|++||+.||++.|.+++|+|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee------ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999 3334332      357899999999999999999999999999999999997


Q ss_pred             CCCCC
Q 021295          135 PKKPN  139 (314)
Q Consensus       135 ~~~~~  139 (314)
                      .+...
T Consensus        77 ~~~~~   81 (88)
T d1wg1a_          77 TDALL   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            65443

>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=7e-19  Score=134.26  Aligned_cols=79  Identities=10%  Similarity=0.093  Sum_probs=71.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ..++|||+|||+++++++|+++|++||+|++|.|..      .++||||+|+++++|++||+.||+..|.+++|.|++|.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            457999999999999999999999999999998853      47899999999999999999999999999999999987


Q ss_pred             CCCCC
Q 021295          135 PKKPN  139 (314)
Q Consensus       135 ~~~~~  139 (314)
                      .....
T Consensus        83 ~~~~~   87 (111)
T d1whxa_          83 IGVFG   87 (111)
T ss_dssp             TTTTC
T ss_pred             CCccc
Confidence            65433

>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=99.75  E-value=1.5e-19  Score=127.14  Aligned_cols=71  Identities=14%  Similarity=0.467  Sum_probs=68.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        59 l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      |||+|||+++||++|+++|++||+|..+++++++.++++++||||+|+++++|++|++.||+..|.++.|+
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            89999999999999999999999999999999999999999999999999999999999999999988764

>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=99.75  E-value=1.6e-18  Score=126.74  Aligned_cols=79  Identities=18%  Similarity=0.282  Sum_probs=70.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee-CCeEEEEee
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL-AGAQVEVKK  132 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~-~gr~l~V~~  132 (314)
                      +++++|||+|||++++|++|+++|++||.|+++.++.+    +.++||||+|+++++|.+|+..||+..| ++++|+|++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            45789999999999999999999999999998877654    3578999999999999999999999888 589999999


Q ss_pred             cCCC
Q 021295          133 AEPK  136 (314)
Q Consensus       133 a~~~  136 (314)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

>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=99.75  E-value=4.3e-18  Score=128.38  Aligned_cols=85  Identities=18%  Similarity=0.237  Sum_probs=74.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc--CCeeeCCeEE
Q 021295           51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQV  128 (314)
Q Consensus        51 ~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l--~~~~~~gr~l  128 (314)
                      .+..++++|||.|||++++|+||+++|++||+|++|+|+++      |++|||+|+++++|++||+.|  +.+.+.+++|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            35567899999999999999999999999999999999754      679999999999999999976  6678899999


Q ss_pred             EEeecCCCCCCCC
Q 021295          129 EVKKAEPKKPNLP  141 (314)
Q Consensus       129 ~V~~a~~~~~~~~  141 (314)
                      +|.+++.++...+
T Consensus        84 ~v~~s~~~~~~~~   96 (104)
T d1wexa_          84 FFNYSTSKRITRP   96 (104)
T ss_dssp             EEEECSSSSCCCS
T ss_pred             EEEEcCCCccCCC
Confidence            9999987665443

>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=99.75  E-value=1.3e-18  Score=124.62  Aligned_cols=76  Identities=20%  Similarity=0.356  Sum_probs=69.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      .+.++|||.||+  +||++|+++|++||+|++|+|.++      ++||||+|+++++|++|++.||+..|.+++|+|++|
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356899999996  899999999999999999999754      569999999999999999999999999999999999


Q ss_pred             CCCC
Q 021295          134 EPKK  137 (314)
Q Consensus       134 ~~~~  137 (314)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8653

>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=99.75  E-value=1.9e-18  Score=128.65  Aligned_cols=80  Identities=21%  Similarity=0.395  Sum_probs=71.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCC--eEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~g--r~l~  129 (314)
                      +..++++|||.|||++++|++|+++|++||+|+.|+|+++      ++||||+|+++++|++|++.||+.+|.+  ++|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEE
Confidence            3456789999999999999999999999999999999865      5699999999999999999999999976  5899


Q ss_pred             EeecCCCC
Q 021295          130 VKKAEPKK  137 (314)
Q Consensus       130 V~~a~~~~  137 (314)
                      |++|++.+
T Consensus        87 v~~ak~~~   94 (97)
T d1whya_          87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99998643

>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=99.75  E-value=2.8e-18  Score=121.48  Aligned_cols=74  Identities=14%  Similarity=0.252  Sum_probs=68.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ++|||+|||+++++++|+++|++||+|+.|+|+.++..  .++||||+|+++++|++||+ +|...|++++|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999998654  45799999999999999996 6899999999999875

>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=99.75  E-value=2.3e-18  Score=128.37  Aligned_cols=78  Identities=18%  Similarity=0.295  Sum_probs=71.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ....+|||.|||++++++||+++|++||+|+.|+|.+       ++||||+|.++++|++||++||+..|.++.|+|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3567899999999999999999999999999999863       479999999999999999999999999999999998


Q ss_pred             CCCCC
Q 021295          134 EPKKP  138 (314)
Q Consensus       134 ~~~~~  138 (314)
                      +.+..
T Consensus        86 ~~~~~   90 (98)
T d1wg4a_          86 RVYPE   90 (98)
T ss_dssp             EEECC
T ss_pred             ecCCC
Confidence            76543

>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=99.74  E-value=1.7e-18  Score=130.35  Aligned_cols=81  Identities=12%  Similarity=0.131  Sum_probs=72.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ...+|||+|||+++|++||+++|+.|+.|+.+.++.+..+++++|||||+|+++++|++||+ ||+..|.++.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            45789999999999999999999999999876566666789999999999999999999996 79999999999999886


Q ss_pred             CC
Q 021295          135 PK  136 (314)
Q Consensus       135 ~~  136 (314)
                      .+
T Consensus        86 ~~   87 (103)
T d2cpya1          86 LE   87 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=99.74  E-value=1.3e-18  Score=128.01  Aligned_cols=81  Identities=17%  Similarity=0.413  Sum_probs=72.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHH----HHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEE
Q 021295           55 KTKKIFVGGIPSSVNEDEFKD----FFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV  130 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~----~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V  130 (314)
                      ++++|||+|||++++|+||++    +|++||+|++|.|..   +.++++||||+|+++++|++|++.||+..|.+++|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            468999999999999999864    579999999998864   4567899999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 021295          131 KKAEPKKP  138 (314)
Q Consensus       131 ~~a~~~~~  138 (314)
                      .+|+++..
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99987643

>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=99.74  E-value=3.5e-18  Score=129.78  Aligned_cols=84  Identities=12%  Similarity=0.157  Sum_probs=74.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee--CCeEEEEe
Q 021295           54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL--AGAQVEVK  131 (314)
Q Consensus        54 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~--~gr~l~V~  131 (314)
                      .++.+|||+|||+++||++|+++|++||+|++|.|++++    .+++|||+|+++++|++||+.||+..|  .+++|+|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            457789999999999999999999999999999999774    589999999999999999999999888  57889999


Q ss_pred             ecCCCCCCCC
Q 021295          132 KAEPKKPNLP  141 (314)
Q Consensus       132 ~a~~~~~~~~  141 (314)
                      +++++.....
T Consensus        81 ~s~~~~~~~~   90 (108)
T d2adba1          81 FSKLTSLNVK   90 (108)
T ss_dssp             ECSSCSCCCC
T ss_pred             ecCCcccccc
Confidence            9887655433

>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=99.73  E-value=7.5e-18  Score=123.08  Aligned_cols=81  Identities=16%  Similarity=0.282  Sum_probs=72.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc--CCeeeCCeEEE
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQVE  129 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l--~~~~~~gr~l~  129 (314)
                      +..++++|||+|||+++++++|+++|++||.|++|+++++      +++|||+|+++++|++|++.+  +...|.+++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3567899999999999999999999999999999999865      469999999999999999864  67899999999


Q ss_pred             EeecCCCCC
Q 021295          130 VKKAEPKKP  138 (314)
Q Consensus       130 V~~a~~~~~  138 (314)
                      |.+++.+..
T Consensus        78 v~~sk~~~l   86 (88)
T d2cq1a1          78 IQYSNHKEL   86 (88)
T ss_dssp             EEECSCSSC
T ss_pred             EEECCCCCC
Confidence            999987654

>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=2.9e-18  Score=131.04  Aligned_cols=84  Identities=18%  Similarity=0.313  Sum_probs=75.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ...+..+|||.|||+++||+||+++|+.++.|+.+.++.+..+++++|+|||+|.++++|++||+ ||+..|.++.|.|.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            34456799999999999999999999999999876676666789999999999999999999996 79999999999999


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      .+.++
T Consensus        93 ~~~~~   97 (112)
T d1wela1          93 PITKK   97 (112)
T ss_dssp             EECHH
T ss_pred             EcChH
Confidence            88654

>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=99.71  E-value=8.1e-18  Score=125.62  Aligned_cols=81  Identities=20%  Similarity=0.303  Sum_probs=72.1

Q ss_pred             CCCCcceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHH--hcCCeeeCCeEE
Q 021295           52 KDFKTKKIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA--KGNKLELAGAQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~-~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~--~l~~~~~~gr~l  128 (314)
                      ....+++|||.|||.+ +||++|.++|++||+|++|.|+++      +++|||+|+++++|++|++  .++.+.|.+++|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            4456789999999985 899999999999999999999865      5799999999999999998  468899999999


Q ss_pred             EEeecCCCCC
Q 021295          129 EVKKAEPKKP  138 (314)
Q Consensus       129 ~V~~a~~~~~  138 (314)
                      +|.+++.++.
T Consensus        88 ~V~~s~~~~~   97 (99)
T d1x4fa1          88 KVDLSEKYKK   97 (99)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEEcCCccc
Confidence            9999987653

>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=99.70  E-value=3.9e-17  Score=115.50  Aligned_cols=71  Identities=15%  Similarity=0.347  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecCCC
Q 021295           59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  136 (314)
Q Consensus        59 l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~~~  136 (314)
                      |||+|||++++++||+++|++|| |+.+.+.      ++++||||+|++.++|++|++.||+..|.+++|+|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999998 5555543      35789999999999999999999999999999999999754

>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=99.68  E-value=5.5e-19  Score=129.79  Aligned_cols=79  Identities=16%  Similarity=0.392  Sum_probs=68.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEe-----ecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEe
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM-----RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK  131 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~-----~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~  131 (314)
                      ++|||+|||+++||++|+++|++++.|..+.+.     .+..+.++++||||+|+++++|++|++ ||++.|.+++|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            689999999999999999999999987655443     445677899999999999999999985 89999999999998


Q ss_pred             ecCCC
Q 021295          132 KAEPK  136 (314)
Q Consensus       132 ~a~~~  136 (314)
                      .+++.
T Consensus        81 r~k~~   85 (90)
T d1u2fa_          81 RPHDY   85 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            65543

>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=99.68  E-value=6.3e-17  Score=118.26  Aligned_cols=80  Identities=14%  Similarity=0.161  Sum_probs=71.2

Q ss_pred             CCCCcceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc--CCeeeCCeEE
Q 021295           52 KDFKTKKIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQV  128 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~-~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l--~~~~~~gr~l  128 (314)
                      ....+++|||.|||.. +|++||.++|++||+|++|.|+++      +.+|||+|++.++|++|++.|  +...+.+++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            3456789999999986 789999999999999999999876      358999999999999999965  7889999999


Q ss_pred             EEeecCCCC
Q 021295          129 EVKKAEPKK  137 (314)
Q Consensus       129 ~V~~a~~~~  137 (314)
                      +|++|+..+
T Consensus        78 ~V~~s~~~~   86 (89)
T d1x4da1          78 RVHLSQKYK   86 (89)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCcc
Confidence            999998654

>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=99.68  E-value=6.9e-17  Score=121.45  Aligned_cols=79  Identities=16%  Similarity=0.188  Sum_probs=70.2

Q ss_pred             CcceEEEcCCCCCC-CH----HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEE
Q 021295           55 KTKKIFVGGIPSSV-NE----DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE  129 (314)
Q Consensus        55 ~~~~l~V~nLp~~~-~e----~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~  129 (314)
                      .+.+|||.||+.++ ++    ++|+++|++||+|+++.+++      ++++|||+|+++++|++||+.||+..|.+++|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            46789999999986 43    56899999999999999985      367999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 021295          130 VKKAEPKKPN  139 (314)
Q Consensus       130 V~~a~~~~~~  139 (314)
                      |.+|+++...
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999877553

>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=99.60  E-value=7e-17  Score=121.41  Aligned_cols=76  Identities=13%  Similarity=0.233  Sum_probs=71.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      +.|+|.+++.+++|++|+++|++||+|++|+|+++ .+++++|+|||+|++.++|++|++.||+.+|++++|+|++.
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            56889999999999999999999999999999877 58899999999999999999999999999999999999874

>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=99.54  E-value=7.1e-15  Score=109.67  Aligned_cols=66  Identities=14%  Similarity=0.264  Sum_probs=59.3

Q ss_pred             CCCCcceEEEcC--CCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeee
Q 021295           52 KDFKTKKIFVGG--IPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL  123 (314)
Q Consensus        52 ~~~~~~~l~V~n--Lp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~  123 (314)
                      ...++++|+|.|  ||.++||++|+++|++||+|++|.++++      ++||||+|++.++|++|++.||+..|
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345678899965  9999999999999999999999998765      56999999999999999999999876

>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=99.54  E-value=9.7e-15  Score=120.41  Aligned_cols=83  Identities=33%  Similarity=0.656  Sum_probs=74.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.++|||+|||+++||++|+++|++||+|++|.|+++..+++++++|||+|.++++|++|++. +...+..+.+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            458999999999999999999999999999999999999999999999999999999999998 4566788888887765


Q ss_pred             CCCC
Q 021295          135 PKKP  138 (314)
Q Consensus       135 ~~~~  138 (314)
                      +...
T Consensus        84 ~~~~   87 (183)
T d1u1qa_          84 SRED   87 (183)
T ss_dssp             CTTG
T ss_pred             hccc
Confidence            5543

>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=99.53  E-value=1.4e-14  Score=107.69  Aligned_cols=83  Identities=10%  Similarity=0.250  Sum_probs=71.1

Q ss_pred             CCCCcceEEEcCC--CCCCC---------HHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCC
Q 021295           52 KDFKTKKIFVGGI--PSSVN---------EDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK  120 (314)
Q Consensus        52 ~~~~~~~l~V~nL--p~~~~---------e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~  120 (314)
                      +...+++|+|.||  |.++.         ++||++.|++||+|+.|.|+.+    +++|+|||+|+++++|++|++.||+
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            4557899999999  55432         3688899999999999998765    3679999999999999999999999


Q ss_pred             eeeCCeEEEEeecCCCCC
Q 021295          121 LELAGAQVEVKKAEPKKP  138 (314)
Q Consensus       121 ~~~~gr~l~V~~a~~~~~  138 (314)
                      ..|++++|.|+++.++..
T Consensus        80 ~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          80 RWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             cEECCEEEEEEEeCCcCC
Confidence            999999999999887653

>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=99.52  E-value=5.3e-15  Score=112.73  Aligned_cols=74  Identities=16%  Similarity=0.191  Sum_probs=63.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCCh-HHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-QAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        56 ~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~-~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      ...+||+|||+++||++|+++|++||+|+.|+|+++      ++||||+|+++ ++|.+|++.|+...|..+.+.|.++.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            346699999999999999999999999999999854      68999999996 78999999999888877666666554


Q ss_pred             C
Q 021295          135 P  135 (314)
Q Consensus       135 ~  135 (314)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.45  E-value=6.8e-14  Score=99.76  Aligned_cols=74  Identities=16%  Similarity=0.242  Sum_probs=63.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeE-EEEeec
Q 021295           55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ-VEVKKA  133 (314)
Q Consensus        55 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~-l~V~~a  133 (314)
                      +.+.|+|.+||++++++.| ++|++||+|+++++.+      .++||||+|+++++|++||+ +|+..|.++. |.|+.+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            4678999999999987655 5799999999998754      36799999999999999996 7999999985 568887


Q ss_pred             CCC
Q 021295          134 EPK  136 (314)
Q Consensus       134 ~~~  136 (314)
                      .++
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            764

>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=99.41  E-value=8e-14  Score=104.44  Aligned_cols=82  Identities=17%  Similarity=0.220  Sum_probs=69.9

Q ss_pred             CCcceEEEcCC--CCCCC--------HHHHHHHHhccCCeEEEEEeecCCC--CCcceEEEEEeCChHHHHHHHHhcCCe
Q 021295           54 FKTKKIFVGGI--PSSVN--------EDEFKDFFMQFGDVQEHQIMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKL  121 (314)
Q Consensus        54 ~~~~~l~V~nL--p~~~~--------e~~l~~~F~~~G~v~~v~i~~~~~~--g~~rG~afV~F~~~~~a~~a~~~l~~~  121 (314)
                      .+++.|.|.||  |.++.        .+||++.|++||+|++|.|+++..+  ...++++||+|+++++|.+|++.||+.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35788999999  55543        3678999999999999999887654  335689999999999999999999999


Q ss_pred             eeCCeEEEEeecCC
Q 021295          122 ELAGAQVEVKKAEP  135 (314)
Q Consensus       122 ~~~gr~l~V~~a~~  135 (314)
                      .+++|+|+|.++.+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999998764

>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=98.86  E-value=1.1e-09  Score=79.21  Aligned_cols=48  Identities=35%  Similarity=0.607  Sum_probs=43.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+.|+++||||||+|.++++|++||++.+.|+++.|.|+++.+++.
T Consensus        41 ~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          41 KKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             EECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCC
T ss_pred             ccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCCCCC
Confidence            468899999999999999999999999988899999999999887654

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=9.8e-09  Score=72.66  Aligned_cols=47  Identities=23%  Similarity=0.547  Sum_probs=42.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |+|+.|++++|||||+|.++++|++||+  +...+.+++|.|+++.+++
T Consensus        32 ~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1          32 MRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             CCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             EeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            5688999999999999999999999998  5558999999999988664

>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=98.67  E-value=9.7e-09  Score=71.30  Aligned_cols=43  Identities=44%  Similarity=0.783  Sum_probs=38.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|+++||||||+|.++++|++||+ +.+.|.++.|.|+++
T Consensus        32 ~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          32 KLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             ccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            5788999999999999999999999999 556899999998764

>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=98.67  E-value=9.6e-09  Score=72.99  Aligned_cols=44  Identities=45%  Similarity=0.783  Sum_probs=40.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      |+|+.|+++||||||+|.++++|++|++ +.+.|.++.|.|+++.
T Consensus        39 ~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          39 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             cccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4788999999999999999999999998 6678999999999875

>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=98.66  E-value=2.8e-08  Score=72.76  Aligned_cols=49  Identities=24%  Similarity=0.425  Sum_probs=43.0

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++||||||+|.+.++|++||+.  ...|.++.|.|+++.++...
T Consensus        41 ~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          41 PIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             cccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCcc
Confidence            47889999999999999999999999984  45899999999998876543

>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=98.65  E-value=1.5e-08  Score=73.32  Aligned_cols=47  Identities=32%  Similarity=0.564  Sum_probs=42.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |+|+.|+++||||||+|.+.++|++||+  +...|.++.|.|+++.++.
T Consensus        42 ~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          42 PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             eecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            5788999999999999999999999998  5558999999999988764

>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=98.64  E-value=5.5e-09  Score=72.99  Aligned_cols=43  Identities=42%  Similarity=0.707  Sum_probs=39.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      ++|+.|+++||||||+|+++++|++|++ +.+.|+++.|.|+.+
T Consensus        33 ~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          33 MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             ECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             ecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4789999999999999999999999998 667899999999875

>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=98.63  E-value=8.8e-09  Score=71.56  Aligned_cols=43  Identities=35%  Similarity=0.546  Sum_probs=38.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      |+|+.|+++||||||+|++.++|++||+ +.+.|.++.|+|+.+
T Consensus        32 ~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          32 PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             cccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            5789999999999999999999999998 556899999988753

>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=98.62  E-value=1.7e-08  Score=72.62  Aligned_cols=47  Identities=21%  Similarity=0.425  Sum_probs=41.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~   47 (314)
                      ++|+.|+++||||||+|.+.++|++||+.+  ..+.++.|.|+++.|+.
T Consensus        41 ~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          41 AKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             EECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             cccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            467889999999999999999999999844  58999999999988764

>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=98.61  E-value=1.3e-08  Score=73.00  Aligned_cols=46  Identities=24%  Similarity=0.390  Sum_probs=41.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|++.++|++|++  +...+.++.|.|+++.++
T Consensus        40 ~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          40 NLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             EECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             cccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            4688999999999999999999999998  456899999999998765

>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=98.60  E-value=2.5e-08  Score=71.49  Aligned_cols=46  Identities=22%  Similarity=0.391  Sum_probs=41.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|.+.++|++|++  +...|.++.|.|+++.|+
T Consensus        38 ~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1          38 PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             ccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            5788999999999999999999999998  456899999999998765

>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=98.60  E-value=4.2e-08  Score=72.33  Aligned_cols=47  Identities=34%  Similarity=0.693  Sum_probs=41.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc-CccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~-~~i~g~~i~v~~~~~~~   47 (314)
                      |+|+.|+++||||||+|.+.++|++||+.+ ..|.++.|.|+++.++.
T Consensus        43 ~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          43 ITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGA   90 (103)
T ss_dssp             SCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTTC
T ss_pred             cccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCCCC
Confidence            578899999999999999999999999943 47899999999887653

>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=98.59  E-value=2.2e-08  Score=73.95  Aligned_cols=48  Identities=38%  Similarity=0.698  Sum_probs=42.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~   48 (314)
                      ++|+.|+.+||||||+|.+.++|++||+ +.+.|+++.|.|+++.+++.
T Consensus        53 ~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          53 MRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE  101 (103)
T ss_dssp             ECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCC
T ss_pred             cccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcccCC
Confidence            3688999999999999999999999998 55688999999999887754

>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=98.58  E-value=2.2e-08  Score=70.61  Aligned_cols=45  Identities=24%  Similarity=0.505  Sum_probs=40.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      ++|+.|+++|+||||+|+++++|++|++  +...+.++.|.|+++.|
T Consensus        35 ~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          35 MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4678899999999999999999999998  55689999999998864

>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=98.58  E-value=2.7e-08  Score=70.69  Aligned_cols=47  Identities=28%  Similarity=0.524  Sum_probs=41.7

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      |+|+.|+++|+||||+|.++++|++|++  +...|.+++|.|+++.+..
T Consensus        34 ~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          34 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             ECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             eccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            4789999999999999999999999999  4558999999999987643

>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=98.56  E-value=2.8e-08  Score=73.18  Aligned_cols=48  Identities=25%  Similarity=0.484  Sum_probs=42.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      |+|+.|+++||||||+|+++++|++||+  +...|.++.|.|+++.++..
T Consensus        51 ~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          51 FIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             EECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             eeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            4678999999999999999999999997  55689999999999887654

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.53  E-value=6.5e-08  Score=70.83  Aligned_cols=49  Identities=27%  Similarity=0.514  Sum_probs=42.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|+.|+++++||||+|.+.++|++||+  +...|.++.|.|+++.++...
T Consensus        49 ~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          49 YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM   99 (101)
T ss_dssp             CBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             eeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            3678899999999999999999999998  556899999999998876543

>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=98.52  E-value=3.6e-08  Score=69.19  Aligned_cols=44  Identities=23%  Similarity=0.532  Sum_probs=39.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      |+|+.|+++++||||+|.++++|++|++  +...+.+++|+|+++.
T Consensus        33 ~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          33 CRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4788999999999999999999999998  4558899999998874

>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=98.52  E-value=6.2e-08  Score=69.45  Aligned_cols=49  Identities=27%  Similarity=0.544  Sum_probs=42.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+++.+++++|||||+|.++++|++|++  +...|.++.|.|+++.++...
T Consensus        38 ~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~~   88 (90)
T d1x5sa1          38 VKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   88 (90)
T ss_dssp             CCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             ccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCCC
Confidence            4677899999999999999999999997  566899999999998776543

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.52  E-value=5.3e-08  Score=69.30  Aligned_cols=44  Identities=5%  Similarity=0.309  Sum_probs=37.1

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      ++.++++||||||+|++.++|++|++ +.+.+.++.|.|+++.++
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            56799999999999999999999998 666899999999998765

>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=98.49  E-value=8.7e-08  Score=70.68  Aligned_cols=50  Identities=18%  Similarity=0.308  Sum_probs=43.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+++.++++||||||+|+++++|++|++ +.+.|.++.|.|.++.+++...
T Consensus        48 ~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~~~~~~   98 (104)
T d1wg5a_          48 LPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRT   98 (104)
T ss_dssp             CCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTTSCC
T ss_pred             EEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCHHHhcc
Confidence            4567799999999999999999999998 6678999999999988775443

>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=98.48  E-value=2.7e-08  Score=73.13  Aligned_cols=45  Identities=16%  Similarity=0.369  Sum_probs=40.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      |+|+.|+++||||||+|+++++|++|++ +...|.++.|.|+++.+
T Consensus        51 ~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          51 ISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             CCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             eecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCC
Confidence            5788999999999999999999999998 55689999999998754

>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=98.47  E-value=7e-08  Score=67.84  Aligned_cols=45  Identities=33%  Similarity=0.668  Sum_probs=40.3

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      ++|+.++++++||||+|.++++|++|++  +...+.++.|.|+++.|
T Consensus        35 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          35 VRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            3678899999999999999999999998  55689999999999865

>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=98.47  E-value=5.3e-08  Score=75.75  Aligned_cols=49  Identities=27%  Similarity=0.426  Sum_probs=42.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      |+|+.|+++||||||+|.+.++|++||+  +.+.|.++.|.|+++.++...
T Consensus        75 ~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~~  125 (139)
T d1u6fa1          75 VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             EEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             ccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            4688899999999999999999999998  446899999999998766543

>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=98.46  E-value=1.1e-07  Score=68.69  Aligned_cols=46  Identities=13%  Similarity=0.218  Sum_probs=40.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|.+.++|++|++  +...|.++.|.|+++...
T Consensus        40 ~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~   87 (93)
T d1h2vz_          40 GLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF   87 (93)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCC
T ss_pred             ccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4688999999999999999999999998  555889999999998654

>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=98.45  E-value=1.5e-07  Score=67.97  Aligned_cols=47  Identities=23%  Similarity=0.425  Sum_probs=39.9

Q ss_pred             CCC-CCCCcccEEEEEECCHHHHHHHHHc---cCccCCcEEEEeecCCCCC
Q 021295            2 KDR-KTGQPRGFGFVTYADPSVVDKVIED---THIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~-~tg~~kG~aFV~f~~~~~a~~A~~~---~~~i~g~~i~v~~~~~~~~   48 (314)
                      +|+ .|+++||||||+|.+.++|++||+.   ...|.+++|.|+++.++..
T Consensus        42 ~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          42 KKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             CCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             eccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCCC
Confidence            454 4899999999999999999999984   3579999999999877643

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=98.45  E-value=4.9e-08  Score=70.30  Aligned_cols=46  Identities=22%  Similarity=0.513  Sum_probs=39.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~   46 (314)
                      |+++.|+++||||||+|.+.++|++||+ +...|.++.|.|+++.++
T Consensus        45 v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          45 VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             CCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCS
T ss_pred             eeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecCCC
Confidence            3456799999999999999999999998 566899999999987653

>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=98.44  E-value=8.7e-08  Score=67.24  Aligned_cols=45  Identities=16%  Similarity=0.265  Sum_probs=34.2

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~   45 (314)
                      |++++++++|+||||+|.+.++|++|++  +...+.+++|.|+++.|
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            4567899999999999999999999998  56689999999998876

>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=98.43  E-value=5.8e-08  Score=71.63  Aligned_cols=46  Identities=24%  Similarity=0.618  Sum_probs=40.4

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      |+|+.|+++||||||+|.+.++|++|++  +...|.++.|.|+++.++
T Consensus        41 ~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          41 VYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             EEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             ccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            4678899999999999999999999998  445899999999987654

>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=98.43  E-value=9.7e-08  Score=66.61  Aligned_cols=43  Identities=40%  Similarity=0.822  Sum_probs=38.6

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      .|+.|++++|||||+|.++++|++|++ +.+.|.+++|.|+++.
T Consensus        36 ~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A~   79 (79)
T d1l3ka2          36 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL   79 (79)
T ss_dssp             ECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             cCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            578899999999999999999999998 6678999999998763

>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=98.42  E-value=1.2e-07  Score=65.28  Aligned_cols=43  Identities=49%  Similarity=0.758  Sum_probs=38.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      ++++.|+.+++||||+|.+.++|++|++ +.+.|+++.|+|+++
T Consensus        32 ~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          32 MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             BCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             eeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            4678899999999999999999999998 567899999999874

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.40  E-value=2e-07  Score=68.60  Aligned_cols=46  Identities=11%  Similarity=0.309  Sum_probs=39.8

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ..++++||||||+|.+.++|++|++ +.+.|.++.|.|+++.++...
T Consensus        51 ~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~~~~~~   97 (104)
T d1wi8a_          51 SNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             SCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCCC
T ss_pred             ccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            3589999999999999999998887 667899999999998776543

>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=98.39  E-value=1.2e-07  Score=67.22  Aligned_cols=43  Identities=28%  Similarity=0.588  Sum_probs=35.6

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--CccCC--cEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIING--KQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g--~~i~v~~~   43 (314)
                      |+|+.|+++||||||+|.+.++|++|++.+  ..+.+  ++|.|+++
T Consensus        39 ~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          39 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            468899999999999999999999999843  45554  77888764

>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=98.39  E-value=3.5e-07  Score=66.26  Aligned_cols=50  Identities=20%  Similarity=0.298  Sum_probs=40.4

Q ss_pred             CCCC-CCCCcccEEEEEECCHHHHHHHHHcc----CccCCcEEEEeecCCCCCCC
Q 021295            1 MKDR-KTGQPRGFGFVTYADPSVVDKVIEDT----HIINGKQVEIKRTIPKGAVG   50 (314)
Q Consensus         1 m~d~-~tg~~kG~aFV~f~~~~~a~~A~~~~----~~i~g~~i~v~~~~~~~~~~   50 (314)
                      |+|. .++++||||||+|.+.++|++|++.+    ..+.++.|.|+++.|+....
T Consensus        35 ~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~~   89 (96)
T d2disa1          35 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVD   89 (96)
T ss_dssp             CSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCSTT
T ss_pred             eeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCCC
Confidence            3454 47899999999999999999999844    25578999999998776543

>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=98.34  E-value=4.1e-07  Score=65.97  Aligned_cols=48  Identities=13%  Similarity=0.381  Sum_probs=40.5

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHcc--------CccCCcEEEEeecCCCCC
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT--------HIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--------~~i~g~~i~v~~~~~~~~   48 (314)
                      ++++.++++||||||+|.+.++|++||+.+        ..+.++.|.|+++.++..
T Consensus        41 ~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          41 VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             CBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             ccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCCc
Confidence            467789999999999999999999999843        267889999999877643

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.32  E-value=1.8e-07  Score=66.18  Aligned_cols=39  Identities=28%  Similarity=0.647  Sum_probs=34.3

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      ++||||||+|++.++|++|++  +.+.+.++.|.|+++.+.
T Consensus        41 ~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          41 LSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             ccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            689999999999999999998  456899999999987543

>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=98.32  E-value=1.6e-07  Score=68.99  Aligned_cols=45  Identities=18%  Similarity=0.176  Sum_probs=39.9

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      .+++++|||||+|+++++|++|++ +.+.|.++.|+|.++.++...
T Consensus        50 ~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          50 PDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             SSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCCCC
T ss_pred             cCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcCCCCCC
Confidence            578999999999999999999998 667999999999998876544

>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=98.30  E-value=2.2e-07  Score=65.46  Aligned_cols=40  Identities=20%  Similarity=0.525  Sum_probs=34.8

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEE
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEI   40 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v   40 (314)
                      |+|+.|+++|+||||+|.+.++|++|++  +...|.++.|+|
T Consensus        42 ~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          42 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             EECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             cccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4688899999999999999999999997  455788888875

>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=98.30  E-value=4.2e-07  Score=63.15  Aligned_cols=42  Identities=17%  Similarity=0.302  Sum_probs=36.9

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      +| .++++||||||+|.++++|++|++  +...+.+++|.|+.+.
T Consensus        34 ~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          34 YD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CS-SCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             Ee-eccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45 489999999999999999999998  4568999999998865

>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=98.28  E-value=2.7e-07  Score=65.35  Aligned_cols=42  Identities=14%  Similarity=0.070  Sum_probs=36.8

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      +..|+++||||||+|+++++|++||+ +...+.++.|.|+++.
T Consensus        40 ~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          40 RTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             ECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             eeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            34689999999999999999999998 5568899999998754

>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=98.26  E-value=3.5e-07  Score=64.77  Aligned_cols=41  Identities=17%  Similarity=0.327  Sum_probs=36.0

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEee
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR   42 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~   42 (314)
                      ++..|++++|||||+|++.++|++|++  +...|.+++|+|+.
T Consensus        43 ~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1          43 KYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             EECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             EeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            455789999999999999999999998  55688999999875

>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=98.25  E-value=3.8e-07  Score=64.54  Aligned_cols=43  Identities=23%  Similarity=0.483  Sum_probs=34.9

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCC--cEEEEeec
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIING--KQVEIKRT   43 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g--~~i~v~~~   43 (314)
                      |+|+.|+++|+||||+|+++++|++|++.  ...+.+  ++|.|+++
T Consensus        39 ~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          39 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            46888999999999999999999999984  456665  44777654

>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=98.22  E-value=4e-07  Score=66.62  Aligned_cols=47  Identities=21%  Similarity=0.279  Sum_probs=40.6

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      .|+.++++++||||+|.+.++|++||+  +...|.++.|.|+++.++..
T Consensus        52 ~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          52 FRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             EEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             cccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            355689999999999999999999998  45589999999999987643

>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=98.22  E-value=8.9e-07  Score=63.65  Aligned_cols=42  Identities=24%  Similarity=0.601  Sum_probs=36.8

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      ..+|+||||+|.++++|++|++  +...|.++.|.|+++.++..
T Consensus        48 ~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          48 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   91 (93)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCCC
Confidence            3479999999999999999997  56689999999999987644

>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=98.22  E-value=2e-07  Score=69.76  Aligned_cols=67  Identities=15%  Similarity=0.206  Sum_probs=50.0

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFG   81 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G   81 (314)
                      +.++++||||||+|.+.++|++|++  +...|.++.|.|+++.+......            +.....+++|+++.++++
T Consensus        40 ~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~~~------------~~~~~~~~~~~~~~~~~g  107 (114)
T d2f9da1          40 GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQK------------MDTKKKEEQLKLLKEKYG  107 (114)
T ss_dssp             ECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHHTTT------------SCHHHHHHHHHHHHHHHC
T ss_pred             cccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCchhhh------------hHHHHHHHHHHHHHHHhC
Confidence            4577889999999999999999998  55689999999998764322211            112235678888888876


Q ss_pred             C
Q 021295           82 D   82 (314)
Q Consensus        82 ~   82 (314)
                      .
T Consensus       108 ~  108 (114)
T d2f9da1         108 I  108 (114)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=98.20  E-value=3e-07  Score=65.52  Aligned_cols=45  Identities=31%  Similarity=0.466  Sum_probs=39.8

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~   49 (314)
                      .+..+++||||+|++.++|++||++.+.|++++|.|+++.++...
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            456789999999999999999999888999999999998876544

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=6.9e-07  Score=63.67  Aligned_cols=41  Identities=22%  Similarity=0.533  Sum_probs=35.5

Q ss_pred             CCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKG   47 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~   47 (314)
                      ..+|+||||+|++.++|++||+.+  ..|.++.|.|+++.++.
T Consensus        45 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2          45 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            347899999999999999999844  58999999999987654

>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=98.18  E-value=4.7e-07  Score=64.50  Aligned_cols=47  Identities=15%  Similarity=0.162  Sum_probs=39.3

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      ++..+.++|+||||+|.+.++|++|++  +...|.+++|.|+++.++..
T Consensus        32 ~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~   80 (88)
T d1wg1a_          32 KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDAL   80 (88)
T ss_dssp             CCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             eeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            445577899999999999999999998  45589999999999865533

>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=98.16  E-value=7.6e-07  Score=62.14  Aligned_cols=47  Identities=23%  Similarity=0.376  Sum_probs=39.1

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHHcc--C-ccCCcEEEEeecCCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIEDT--H-IINGKQVEIKRTIPKGA   48 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~~~--~-~i~g~~i~v~~~~~~~~   48 (314)
                      .+..+.++|+||||+|.++++|++|++.+  . .+.++.|.|+++.++..
T Consensus        29 ~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          29 LAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             EEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            44556778999999999999999999843  3 58999999999987643

>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=98.16  E-value=6.1e-07  Score=65.79  Aligned_cols=43  Identities=16%  Similarity=0.224  Sum_probs=37.2

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      .+..+++++|||||+|.+.++|++||+ +.+.|.++.|.|.++.
T Consensus        42 ~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          42 LVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             EeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            456799999999999999999999998 4568999999998654

>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=98.12  E-value=1e-06  Score=63.68  Aligned_cols=45  Identities=22%  Similarity=0.489  Sum_probs=39.5

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~~~   48 (314)
                      +.++++++||||+|.+.++|++|++.  ...|.++.|.|+++.++..
T Consensus        47 ~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          47 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             eecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            46889999999999999999999984  4589999999999887754

>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=98.11  E-value=8.2e-07  Score=62.80  Aligned_cols=44  Identities=14%  Similarity=0.426  Sum_probs=37.8

Q ss_pred             CCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCCC
Q 021295            5 KTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKGA   48 (314)
Q Consensus         5 ~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~~   48 (314)
                      .+.++|+||||+|.++++|++|++  +...|.++.|.|+++.|++.
T Consensus        39 ~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1          39 RVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             EEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            456789999999999999999998  44589999999999887654

>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=98.11  E-value=8.7e-07  Score=61.05  Aligned_cols=44  Identities=11%  Similarity=0.177  Sum_probs=37.6

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +..+.++|+||||+|.+.++|++|++  +...+.+++|.|+++...
T Consensus        26 ~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          26 YCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             ceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            34567899999999999999999998  445899999999998654

>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=98.10  E-value=2.2e-06  Score=61.11  Aligned_cols=44  Identities=14%  Similarity=0.301  Sum_probs=36.4

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+.+.  ++||||+|++.++|++|++  +.+.|.++.|.|.++.++.
T Consensus        42 ~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          42 TEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             CCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             cccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            455553  8999999999999999998  5558999999999987543

>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=98.07  E-value=5.6e-07  Score=64.46  Aligned_cols=45  Identities=16%  Similarity=0.230  Sum_probs=38.2

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      .+.|+++++||||+|++.++|++|++  +...+.++.|.|+++.++.
T Consensus        39 ~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          39 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   85 (91)
T ss_dssp             CCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             EeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCc
Confidence            34567789999999999999999998  4468999999999987653

>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=98.05  E-value=2.7e-06  Score=61.71  Aligned_cols=39  Identities=21%  Similarity=0.454  Sum_probs=34.4

Q ss_pred             cccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPKG   47 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~~   47 (314)
                      +|+||||+|++.++|++||+.  ...|.++.|.|+++.++.
T Consensus        49 ~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            689999999999999999984  468999999999987543

>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=98.01  E-value=2.1e-06  Score=63.04  Aligned_cols=41  Identities=15%  Similarity=0.266  Sum_probs=36.0

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeec
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRT   43 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~   43 (314)
                      +..|+++||||||+|++.++|++|++  +...+++++|.|+.+
T Consensus        61 ~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          61 DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             CSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             cCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            44699999999999999999999998  556899999988764

>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=98.01  E-value=1e-06  Score=65.66  Aligned_cols=44  Identities=11%  Similarity=0.282  Sum_probs=37.9

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~~   45 (314)
                      ++..+++++|||||+|.+.++|++|++ +.+.|.++.|.|..+.+
T Consensus        52 ~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          52 AYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             EECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECH
T ss_pred             ecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcCh
Confidence            456799999999999999999999998 66689999999886543

>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=98.01  E-value=1.9e-06  Score=59.88  Aligned_cols=45  Identities=20%  Similarity=0.358  Sum_probs=37.5

Q ss_pred             CCCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            3 DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         3 d~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +....++++||||+|++.++|++|++  +...+.+++|.|+++.+++
T Consensus        32 ~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1          32 DLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             eeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            33445678999999999999999998  5568999999999987653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.00  E-value=2.6e-05  Score=55.09  Aligned_cols=69  Identities=6%  Similarity=0.237  Sum_probs=57.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCc--ceEEEEEeCChHHHHHHHHhcCCeeeCC
Q 021295           57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRS--RGFGFITFDTEQAVDDLLAKGNKLELAG  125 (314)
Q Consensus        57 ~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~--rG~afV~F~~~~~a~~a~~~l~~~~~~g  125 (314)
                      ++|.|+.||+.+||+++.+.+...+++.....+.-+.+-++  ---|+|.|.+.+++....+..+++.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            57999999999999999999999988888777766544332  2459999999999999999998877644

>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=97.97  E-value=1.2e-06  Score=59.70  Aligned_cols=38  Identities=24%  Similarity=0.559  Sum_probs=31.1

Q ss_pred             CCCCCCCCcccEEEEEECCHHHHHHHHHc--cCccCCcEE
Q 021295            1 MKDRKTGQPRGFGFVTYADPSVVDKVIED--THIINGKQV   38 (314)
Q Consensus         1 m~d~~tg~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i   38 (314)
                      ++++.|+++++||||+|.+.++|++|++.  ...|.++.|
T Consensus        31 ~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1          31 ILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             ECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             ccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            35778999999999999999999999984  345665544

>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=97.95  E-value=3.3e-07  Score=65.56  Aligned_cols=43  Identities=19%  Similarity=0.403  Sum_probs=36.7

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeecC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTI   44 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~~   44 (314)
                      .++.+.++|+||||+|+++++|++|++ +...+.++.|+|+++.
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            356788999999999999999999987 5668999999997543

>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=97.94  E-value=4.2e-06  Score=60.19  Aligned_cols=43  Identities=16%  Similarity=0.300  Sum_probs=36.7

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      +.+..+|+||||+|++.++|++||+  +.+.|.+++|.|+++.+.
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            3456789999999999999999998  556899999999987643

>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=97.92  E-value=4.6e-06  Score=59.25  Aligned_cols=39  Identities=13%  Similarity=0.325  Sum_probs=31.8

Q ss_pred             CCCCCCCc---ccEEEEEECCHHHHHHHHH--ccCccCCcEEEE
Q 021295            2 KDRKTGQP---RGFGFVTYADPSVVDKVIE--DTHIINGKQVEI   40 (314)
Q Consensus         2 ~d~~tg~~---kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v   40 (314)
                      +|+.|..+   ++||||+|+++++|++|++  +...+.++.|++
T Consensus        45 ~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkv   88 (89)
T d2cpia1          45 NSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA   88 (89)
T ss_dssp             CCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             eccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEE
Confidence            56666554   4999999999999999998  445888988876

>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=97.89  E-value=1.6e-05  Score=55.42  Aligned_cols=54  Identities=15%  Similarity=0.282  Sum_probs=48.5

Q ss_pred             HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeec
Q 021295           71 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA  133 (314)
Q Consensus        71 ~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a  133 (314)
                      ++|.+.|++||+|.-|+++.+        ...|+|.+-++|.+|++. +.+++.++.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l-~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDV-DGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHG-GGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhcc-CCeEEcceEEEEecC
Confidence            567788999999999999987        589999999999999998 899999999999754

>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=97.87  E-value=1.1e-05  Score=59.29  Aligned_cols=38  Identities=18%  Similarity=0.302  Sum_probs=33.1

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      .||||||+|++.++|++||+  +...|.++.|.|+++...
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            37999999999999999998  456889999999987544

>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=97.84  E-value=3e-06  Score=61.76  Aligned_cols=41  Identities=22%  Similarity=0.311  Sum_probs=32.8

Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            4 RKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         4 ~~tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      ..++++++||||+|.+.++|++||+  +...|.++++.+.++.
T Consensus        53 ~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          53 DSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             ccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            3588999999999999999999998  4456777776665443

>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=97.82  E-value=4.7e-06  Score=58.78  Aligned_cols=41  Identities=20%  Similarity=0.425  Sum_probs=35.7

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      -++|+||||+|++.++|++|++  +...|.++.|.|+++.++.
T Consensus        41 ~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          41 HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             ecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3568999999999999999998  4558999999999988764

>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=97.78  E-value=6.4e-06  Score=60.32  Aligned_cols=44  Identities=7%  Similarity=-0.081  Sum_probs=37.1

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHcc--CccCCcEEEEeecCCCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~~--~~i~g~~i~v~~~~~~~~~   49 (314)
                      .-++++||||+|++.++|++|++.+  ..|.++.|.|.++.++...
T Consensus        42 ~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   87 (104)
T d1weya_          42 YFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG   87 (104)
T ss_dssp             EETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSCC
T ss_pred             EecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCCC
Confidence            3467899999999999999999955  4899999999998766443

>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=97.78  E-value=1.6e-05  Score=57.18  Aligned_cols=40  Identities=18%  Similarity=0.307  Sum_probs=34.3

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      ..|+||||+|.+.++|++|++  +...|.++.|+|.++.++.
T Consensus        52 ~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            358999999999999999998  5568899999999876543

>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=97.70  E-value=1.9e-05  Score=54.01  Aligned_cols=36  Identities=8%  Similarity=0.150  Sum_probs=31.1

Q ss_pred             CcccEEEEEECCHHHHHHHHH-ccCccCCcEEEEeec
Q 021295            8 QPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRT   43 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~i~v~~~   43 (314)
                      ..++||||+|+++++|++|++ +.+.|.+++|.|+..
T Consensus        38 ~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          38 KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            345799999999999999998 666899999998864

>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=97.67  E-value=2.3e-05  Score=55.22  Aligned_cols=40  Identities=8%  Similarity=0.153  Sum_probs=33.0

Q ss_pred             CCCcccEEEEEECCHHHHHHHHHcc--Ccc-CCcEEEEeecCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIEDT--HII-NGKQVEIKRTIP   45 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~~~--~~i-~g~~i~v~~~~~   45 (314)
                      +.++++||||+|++.++|++|+..+  ..| +++.|+|.++.+
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            4567899999999999999999843  355 589999988754

>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=97.61  E-value=2.3e-05  Score=57.62  Aligned_cols=40  Identities=8%  Similarity=0.007  Sum_probs=34.5

Q ss_pred             CCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPK   46 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~   46 (314)
                      .++|+||||+|.+.++|++||+  +...|.++.|.|+++...
T Consensus        43 ~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          43 PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            4678999999999999999998  456899999999987544

>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=97.60  E-value=5.6e-05  Score=54.96  Aligned_cols=42  Identities=12%  Similarity=0.131  Sum_probs=34.4

Q ss_pred             CcccEEEEEECCHHHHHHHHHc----cCccCCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIED----THIINGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~----~~~i~g~~i~v~~~~~~~~~   49 (314)
                      ++|++|||+|++.++|++||+.    ...+.+++|+|.++..++..
T Consensus        49 ~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~~   94 (104)
T d1wexa_          49 PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCccC
Confidence            5789999999999999999972    23678999999998765443

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.59  E-value=1.4e-05  Score=55.68  Aligned_cols=44  Identities=14%  Similarity=0.212  Sum_probs=34.5

Q ss_pred             CCCCCCCcccEEEEEECCHHHHHHHHH-ccCccCCcE-EEEeecCC
Q 021295            2 KDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQ-VEIKRTIP   45 (314)
Q Consensus         2 ~d~~tg~~kG~aFV~f~~~~~a~~A~~-~~~~i~g~~-i~v~~~~~   45 (314)
                      .+..+.++|+||||+|+++++|++||+ +...|.++. |.|++...
T Consensus        31 ~~~~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          31 LKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             EEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCC
T ss_pred             heEEecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCC
Confidence            344567889999999999999999998 556787874 56776554

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.58  E-value=4.9e-05  Score=54.85  Aligned_cols=42  Identities=24%  Similarity=0.393  Sum_probs=36.4

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecCCCC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~~~~   47 (314)
                      +.+++|||||+|+++++|++|++  +...+++++|.|+...+++
T Consensus        53 ~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          53 DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcC
Confidence            45788999999999999999998  4458999999999877654

>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=97.57  E-value=0.00024  Score=46.88  Aligned_cols=61  Identities=10%  Similarity=0.158  Sum_probs=51.3

Q ss_pred             HHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhcCCeeeCCeEEEEeecC
Q 021295           71 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE  134 (314)
Q Consensus        71 ~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l~~~~~~gr~l~V~~a~  134 (314)
                      +.|.+.|+++++|..|.|.... .+  .-.|-|..++.++|..|+..||...|..+.|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3445678899999999997653 22  3369999999999999999999999999999999875

>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=97.54  E-value=6.2e-05  Score=55.12  Aligned_cols=42  Identities=14%  Similarity=0.078  Sum_probs=32.8

Q ss_pred             CcccEEEEEECCHHHHHHHHHc--cCcc--CCcEEEEeecCCCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIED--THII--NGKQVEIKRTIPKGAV   49 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~--~~~i--~g~~i~v~~~~~~~~~   49 (314)
                      ++++||||+|+++++|++||+.  ...|  .++.|.+.++.++...
T Consensus        43 ~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~~   88 (108)
T d2adba1          43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN   88 (108)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSCC
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcccc
Confidence            4689999999999999999983  3445  5778888887665443

>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=97.46  E-value=9.1e-05  Score=51.99  Aligned_cols=39  Identities=13%  Similarity=0.172  Sum_probs=33.2

Q ss_pred             CcccEEEEEECCHHHHHHHHHc----cCccCCcEEEEeecCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIED----THIINGKQVEIKRTIPK   46 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~----~~~i~g~~i~v~~~~~~   46 (314)
                      ++++||||+|++.++|++|++.    ...+.+++|.|.++..+
T Consensus        42 ~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1          42 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            5679999999999999999872    34789999999988654

>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=97.45  E-value=3.7e-05  Score=55.46  Aligned_cols=41  Identities=7%  Similarity=0.115  Sum_probs=34.1

Q ss_pred             CCcccEEEEEECCHHHHHHHHH----ccCccCCcEEEEeecCCCC
Q 021295            7 GQPRGFGFVTYADPSVVDKVIE----DTHIINGKQVEIKRTIPKG   47 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~----~~~~i~g~~i~v~~~~~~~   47 (314)
                      -++|+||||+|++.++|++|++    +...+.++.|.|.++..+.
T Consensus        52 ~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          52 MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            3578999999999999999986    3337899999999887654

>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=97.36  E-value=3.8e-05  Score=53.98  Aligned_cols=36  Identities=14%  Similarity=0.180  Sum_probs=29.9

Q ss_pred             cccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            9 PRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      .+|||||+|++.++|++||+  +..+|.++.|.|.+..
T Consensus        34 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1          34 RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            45899999999999999997  5568888888776543

>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=97.27  E-value=4.8e-05  Score=54.75  Aligned_cols=39  Identities=15%  Similarity=0.200  Sum_probs=32.0

Q ss_pred             CcccEEEEEECCHHHHHHHHHc--cCccCCcEEEEeecCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIED--THIINGKQVEIKRTIPK   46 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~~--~~~i~g~~i~v~~~~~~   46 (314)
                      .+++||||+|.++++|++||+.  ..+|.++.|.|.+..++
T Consensus        48 ~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~   88 (98)
T d1wg4a_          48 QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY   88 (98)
T ss_dssp             ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEE
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecC
Confidence            3579999999999999999984  44888888888776544

>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=97.27  E-value=0.00016  Score=51.75  Aligned_cols=39  Identities=8%  Similarity=0.277  Sum_probs=31.0

Q ss_pred             CcccEEEEEECCHHHHHHHHH--ccCccCC--cEEEEeecCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--DTHIING--KQVEIKRTIPK   46 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~~~~i~g--~~i~v~~~~~~   46 (314)
                      ++|+||||+|.+.++|++|++  +..+|.+  ++|.|+++.+.
T Consensus        51 ~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            468899999999999999998  4446655  57888887654

>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=97.18  E-value=0.00019  Score=49.73  Aligned_cols=36  Identities=14%  Similarity=0.154  Sum_probs=29.3

Q ss_pred             cccEEEEEECCHHHHHHHHHcc--Ccc-CCcEEEEeecC
Q 021295            9 PRGFGFVTYADPSVVDKVIEDT--HII-NGKQVEIKRTI   44 (314)
Q Consensus         9 ~kG~aFV~f~~~~~a~~A~~~~--~~i-~g~~i~v~~~~   44 (314)
                      .++||||+|.+.++|++|++.+  ..| .++.|.|.++.
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            5789999999999999999843  355 46788888764

>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=97.16  E-value=0.00025  Score=49.86  Aligned_cols=40  Identities=13%  Similarity=0.199  Sum_probs=33.2

Q ss_pred             CcccEEEEEECCHHHHHHHHH--c--cCccCCcEEEEeecCCCC
Q 021295            8 QPRGFGFVTYADPSVVDKVIE--D--THIINGKQVEIKRTIPKG   47 (314)
Q Consensus         8 ~~kG~aFV~f~~~~~a~~A~~--~--~~~i~g~~i~v~~~~~~~   47 (314)
                      +.+.+|||+|++.++|++|++  +  ...+.+++|.|.++.+..
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            457799999999999999998  2  336899999999987543

>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=96.90  E-value=0.0014  Score=46.05  Aligned_cols=59  Identities=19%  Similarity=0.325  Sum_probs=48.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcceEEEEEeCChHHHHHHHHhc
Q 021295           52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG  118 (314)
Q Consensus        52 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~~~~g~~rG~afV~F~~~~~a~~a~~~l  118 (314)
                      ..+....||.-.+|.++...||.++|+.||.|.-..| .|  |     -|||...+.|.|+.+++.+
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd--T-----Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD--T-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET--T-----EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC--c-----eEEEEecCHHHHHHHHHHh
Confidence            3445568999999999999999999999999875555 33  3     7999999999998888764

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.69  E-value=0.00095  Score=48.15  Aligned_cols=39  Identities=15%  Similarity=0.058  Sum_probs=32.7

Q ss_pred             CCCcccEEEEEECCHHHHHHHHH--ccCccCCcEEEEeecC
Q 021295            6 TGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKRTI   44 (314)
Q Consensus         6 tg~~kG~aFV~f~~~~~a~~A~~--~~~~i~g~~i~v~~~~   44 (314)
                      ....+|++||+|+++++|.+|++  +...++++.|.+....
T Consensus        54 ~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          54 EVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             SCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             ccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            34567999999999999999999  4458899999988754

>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=96.13  E-value=0.0022  Score=45.88  Aligned_cols=24  Identities=8%  Similarity=0.207  Sum_probs=21.1

Q ss_pred             CCcccEEEEEECCHHHHHHHHHcc
Q 021295            7 GQPRGFGFVTYADPSVVDKVIEDT   30 (314)
Q Consensus         7 g~~kG~aFV~f~~~~~a~~A~~~~   30 (314)
                      -.+|+||||+|++.++|++|++.+
T Consensus        53 ~~~k~~aFV~f~~~e~A~~A~~~l   76 (101)
T d2cq2a1          53 PPNKPYSFARYRTTEESKRAYVTL   76 (101)
T ss_dssp             CTTCSCEEEEESSHHHHHHHHHHT
T ss_pred             ccCccEEEEEECCHHHHHHHHHHh
Confidence            356889999999999999999963

>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=95.33  E-value=0.0043  Score=45.19  Aligned_cols=36  Identities=8%  Similarity=0.113  Sum_probs=24.0

Q ss_pred             CcccEEEEEECCH-HHHHHHHHccC--ccCCcEEEEeec
Q 021295            8 QPRGFGFVTYADP-SVVDKVIEDTH--IINGKQVEIKRT   43 (314)
Q Consensus         8 ~~kG~aFV~f~~~-~~a~~A~~~~~--~i~g~~i~v~~~   43 (314)
                      +.++||||+|+++ ++|.+|+.+++  .+..+.+.|.+.
T Consensus        45 ~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          45 RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            5689999999985 67877887433  444444444443

>d2od6a1 d.58.4.22 (A:1-109) Hypothetical protein GOS_2359375 {environmental samples}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Dimeric alpha+beta barrel
family: Marine metagenome family DABB1
domain: Hypothetical protein GOS 2359375
species: environmental samples

Probab=85.31  E-value=2.4  Score=29.75  Aligned_cols=71  Identities=7%  Similarity=-0.039  Sum_probs=51.0

Q ss_pred             EEEEEECCHHHHHHHHHccCccCCcEEEEeecCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEeec
Q 021295           12 FGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRD   91 (314)
Q Consensus        12 ~aFV~f~~~~~a~~A~~~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~v~~v~i~~~   91 (314)
                      |..++|.++.+.+..+....+                                    .-+++.+.|.+.|-+..+....-
T Consensus         9 ~t~~dF~se~dmel~~~~~e~------------------------------------~~~~~~~~Lk~~Gl~r~~~~~iw   52 (109)
T d2od6a1           9 FTTADFINDVDMELFIDAVEK------------------------------------TAPVWVKEMKSRGLLKFSMNRVW   52 (109)
T ss_dssp             EEEEEESSHHHHHHHHHHHHH------------------------------------HHHHHHHHHHTTTEEEEEEEEEC
T ss_pred             EEEEEcCCHHHHHHHHHHHHH------------------------------------HHHHHHHHHHHcCCceEEEEEEe
Confidence            667889999998888873211                                    12667788888887665443333


Q ss_pred             CCCCCcceEEEEEeCChHHHHHHHHhc
Q 021295           92 HSTSRSRGFGFITFDTEQAVDDLLAKG  118 (314)
Q Consensus        92 ~~~g~~rG~afV~F~~~~~a~~a~~~l  118 (314)
                      ...++.+-..+.||+|+++.++|.+.+
T Consensus        53 Nk~~~fr~~~i~EYkd~~Afk~Cq~i~   79 (109)
T d2od6a1          53 NKGEVFRVVMTYEYKDRASFEANIAYL   79 (109)
T ss_dssp             SSSSCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCcEEEEEEEEECCHHHHHHHHHHH
Confidence            345667878889999999999988764