Psyllid ID: psy6490

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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-------320-------330-------340-------350-------360-------370-------380-------390-------40
Protein Sequence
METMALGGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIFECV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccHHHHHHHHccccccccccccEEEccccccccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccccEEEEEccHHHHHHHHcccccEEccEEccccccccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEEcccHHHHHHHHHccEEEcccEEEEEEcccHHHHHHHccccccEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEcccccccccHHHccccccccHHEEcccccccccccccccccHHHHcccccccccccccccccccccccccHHHcccccccccHHHccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEcccccHHHHcccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccEEccEEcEEEEcccccccccccccHEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccEEccEEcEEEEcccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccEcc
Coil and Loop (DISEMBL)
metmalggapdhheqfngliptmnglvqiphhpglvhlngppppphqlvklngapqvntsppqnailhqqptpqpqqqqqqppqpqprdlqpnsnnqlvlvngkssgdsgrstptgddptsaklfVGGLNVVREAHQLVLVngkssgdsgrstptgddptsaklfvgglswqtSSEKLREYFGMFGAVTDVlimkdpitqrsrgfgfitfaepeTVEKVLKVpihtldgkkidpkhatpknrpkignrtkkifvggvsqdtSAEEVKAYFSQFGKVEETVMLMDQQtkrhrgfgfvtfeneEVVDHICEIHFHMIKNKkveckkaqpKEAVQANLLvgkrvilgplglrmaapapitpaTQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIFECV
Flexible Loop (DISEMBL)
metmalggapdhHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGkssgdsgrstptgddptsAKLFVGGLNVVREAHQLVLvngkssgdsgrstptgddptsakLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIhtldgkkidpkhatpknrpkignrtkkiFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIFECV
Low Complexity Region (SEG)
METMALGGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHqqptpqpqqqqqqppqpqpRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPatqlaalqsqaqaqvqaaaaavaaqnaaavaNYGKIFECV
Disordered region (IsUnstruct)
****************NGLIPTMNGLVQIPHH******************************************************************************************KLFVGGLNVVREAHQLVLV**********************LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD**********************KIFVGGVS****AEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAAL******QVQAAAAAVAAQNAAAVANYGKIFE**
Disordered Region (DISOPRED)
***********HHEQFNGLIPTMNGLVQ******************************************************************NNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGL***********************************FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK****************IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK*****************************************************************ANYGKIFECV
Disordered Region (DISEMBL)
*********PDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAIL**********************LQPNSNNQLVLVNGK*************DPTSAKLFVGGLNVVREAHQLVLVNGK*************DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQL***********************AAVANYGKIFECV
Disordered Region (DISPRO)
*****LGGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQ******APQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDS******GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIFECV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METMALGGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIFECV
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	398	2.2.26 [Sep-21-2011]
Q9VVE5	369	RNA-binding protein Musas	no	N/A	0.444	0.479	0.607	5e-63
Q920Q6	346	RNA-binding protein Musas	yes	N/A	0.464	0.534	0.595	9e-63
Q96DH6	328	RNA-binding protein Musas	yes	N/A	0.464	0.564	0.595	2e-62
O43347	362	RNA-binding protein Musas	no	N/A	0.469	0.516	0.569	2e-60
Q61474	362	RNA-binding protein Musas	no	N/A	0.469	0.516	0.569	3e-60
Q8K3P4	362	RNA-binding protein Musas	yes	N/A	0.469	0.516	0.569	3e-60
Q99383	534	Nuclear polyadenylated RN	yes	N/A	0.422	0.314	0.465	4e-45
Q98SJ2	360	DAZ-associated protein 1	N/A	N/A	0.424	0.469	0.475	6e-45
Q9JII5	406	DAZ-associated protein 1	no	N/A	0.424	0.416	0.472	1e-44
Q96EP5	407	DAZ-associated protein 1	no	N/A	0.424	0.415	0.472	1e-44

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

 Score =  242 bits (617), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 144/181 (79%), Gaps = 4/181 (2%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +DP   K+F+GGLSWQTS E LR+YFG +G +++ ++MKDP T+RSRGFGF+TF++P +V
Sbjct: 26  NDP--GKMFIGGLSWQTSPESLRDYFGRYGDISEAMVMKDPTTRRSRGFGFVTFSDPNSV 83

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK 275
           +KVL    H LDGKK+DPK A P+   PK+  RTKKIFVGG+S  T+ E+VK+YF QFG 
Sbjct: 84  DKVLTQGTHELDGKKVDPKVAFPRRAHPKMVTRTKKIFVGGLSAPTTLEDVKSYFEQFGP 143

Query: 276 VEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQ-AN 334
           +E+ +++ D+QT RHRGFGFVTF++E+VVD +CEIHFH I NK VECKKAQPKE +  AN
Sbjct: 144 IEDAMLMFDKQTNRHRGFGFVTFQSEDVVDKVCEIHFHEINNKMVECKKAQPKEVMLPAN 203

Query: 335 L 335
           L
Sbjct: 204 L 204

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 =  241 bits (614), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 112/188 (59%), Positives = 143/188 (76%), Gaps = 3/188 (1%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           S G SG +  +  DP   K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+RSRG
Sbjct: 6   SPGTSGSANDSQHDP--GKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRG 63

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSA 263
           FGF+TFA+P +V+KVL  P H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T  
Sbjct: 64  FGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSANTVV 123

Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK 323
           E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +CEIHFH I NK VECK
Sbjct: 124 EDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECK 183

Query: 324 KAQPKEAV 331
           KAQPKE +
Sbjct: 184 KAQPKEVM 191

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

Mus musculus (taxid: 10090)

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

 Score =  240 bits (612), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 112/188 (59%), Positives = 143/188 (76%), Gaps = 3/188 (1%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           S G SG +  +  DP   K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+RSRG
Sbjct: 6   SQGTSGSANDSQHDP--GKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRG 63

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSA 263
           FGF+TFA+P +V+KVL  P H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T  
Sbjct: 64  FGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSANTVV 123

Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK 323
           E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +CEIHFH I NK VECK
Sbjct: 124 EDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECK 183

Query: 324 KAQPKEAV 331
           KAQPKE +
Sbjct: 184 KAQPKEVM 191

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

Homo sapiens (taxid: 9606)

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

 Score =  233 bits (594), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 107/188 (56%), Positives = 139/188 (73%), Gaps = 1/188 (0%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL 
Sbjct: 20  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 79

Query: 222 VPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
              H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T+ E+VK YF QFGKV++ +
Sbjct: 80  QSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKQYFEQFGKVDDAM 139

Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
           ++ D+ T RHRGFGFVTFE+E++V+ +CEIHFH I NK VECKKAQPKE +        R
Sbjct: 140 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKEVMSPTGSARGR 199

Query: 341 VILGPLGL 348
             + P G+
Sbjct: 200 SRVMPYGM 207

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

Homo sapiens (taxid: 9606)

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

 Score =  233 bits (593), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 107/188 (56%), Positives = 139/188 (73%), Gaps = 1/188 (0%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL 
Sbjct: 20  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 79

Query: 222 VPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
              H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T+ E+VK YF QFGKV++ +
Sbjct: 80  QSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKHYFEQFGKVDDAM 139

Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
           ++ D+ T RHRGFGFVTFE+E++V+ +CEIHFH I NK VECKKAQPKE +        R
Sbjct: 140 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKEVMSPTGSARGR 199

Query: 341 VILGPLGL 348
             + P G+
Sbjct: 200 SRVMPYGM 207

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

Mus musculus (taxid: 10090)

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

 Score =  233 bits (593), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 107/188 (56%), Positives = 139/188 (73%), Gaps = 1/188 (0%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL 
Sbjct: 20  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 79

Query: 222 VPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
              H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T+ E+VK YF QFGKV++ +
Sbjct: 80  QSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKHYFEQFGKVDDAM 139

Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
           ++ D+ T RHRGFGFVTFE+E++V+ +CEIHFH I NK VECKKAQPKE +        R
Sbjct: 140 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKEVMSPTGSARGR 199

Query: 341 VILGPLGL 348
             + P G+
Sbjct: 200 SRVMPYGM 207

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

Rattus norvegicus (taxid: 10116)

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

 Score =  182 bits (462), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 80/172 (46%), Positives = 122/172 (70%), Gaps = 4/172 (2%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S K+F+GGL+W T+ + LREYFG +G VTD+ IMKDP T RSRGFGF++F +P +V++V+
Sbjct: 158 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 217

Query: 221 KVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
           K   H LDGK IDPK A P++     ++T KIFVGG+  D   +E + +FSQ+G + +  
Sbjct: 218 KTQ-HILDGKVIDPKRAIPRDEQ---DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 273

Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQ 332
           +++D+ T + RGFGFVT+++ + VD +C+  F   K++K+E K+A+P+   Q
Sbjct: 274 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRHMQQ 325

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|Q98SJ2|DAZP1_XENLA DAZ-associated protein 1 OS=Xenopus laevis GN=dazap1 PE=1 SV=1

 Score =  182 bits (461), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 88/185 (47%), Positives = 117/185 (63%), Gaps = 16/185 (8%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            KLFVGGL W T+ E LR YF  +G V D +IMKD  T +SRGFGF+ F +P  V  VL 
Sbjct: 10  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 69

Query: 222 VPIHTLDGKKIDPKHATP------KNRPKIG----------NRTKKIFVGGVSQDTSAEE 265
              HTLDG+ IDPK  TP      ++RP+ G          +R+ KIFVGG+  +    E
Sbjct: 70  SRPHTLDGRNIDPKPCTPRGMQPERSRPREGWQQKEPRTENSRSNKIFVGGIPHNCGETE 129

Query: 266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA 325
           +K YF++FG V E VM+ D + +R RGFGF+TFE+E+ VD    +HFH I  KKVE K+A
Sbjct: 130 LKEYFNRFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA 189

Query: 326 QPKEA 330
           +P+++
Sbjct: 190 EPRDS 194

RNA-binding protein, which is required during gametogenesis. May be involved in the actin-dependent anchoring of Vg1 mRNA in the vegetal cortex of the oocyte.

Xenopus laevis (taxid: 8355)

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

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 87/184 (47%), Positives = 115/184 (62%), Gaps = 15/184 (8%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            KLFVGGL W T+ E LR YF  +G V D +IMKD  T +SRGFGF+ F +P  V  VL 
Sbjct: 10  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 69

Query: 222 VPIHTLDGKKIDPKHATP------KNRPKIG---------NRTKKIFVGGVSQDTSAEEV 266
              HTLDG+ IDPK  TP      + RPK G         +++ KIFVGG+  +    E+
Sbjct: 70  SRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDSSKSNKIFVGGIPHNCGETEL 129

Query: 267 KAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ 326
           + YF +FG V E VM+ D + +R RGFGF+TFE+E+ VD    +HFH I  KKVE K+A+
Sbjct: 130 REYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAE 189

Query: 327 PKEA 330
           P+++
Sbjct: 190 PRDS 193

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

Mus musculus (taxid: 10090)

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

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 87/184 (47%), Positives = 115/184 (62%), Gaps = 15/184 (8%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            KLFVGGL W T+ E LR YF  +G V D +IMKD  T +SRGFGF+ F +P  V  VL 
Sbjct: 10  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 69

Query: 222 VPIHTLDGKKIDPKHATP------KNRPKIG---------NRTKKIFVGGVSQDTSAEEV 266
              HTLDG+ IDPK  TP      + RPK G         +++ KIFVGG+  +    E+
Sbjct: 70  SRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDNSKSNKIFVGGIPHNCGETEL 129

Query: 267 KAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ 326
           + YF +FG V E VM+ D + +R RGFGF+TFE+E+ VD    +HFH I  KKVE K+A+
Sbjct: 130 REYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAE 189

Query: 327 PKEA 330
           P+++
Sbjct: 190 PRDS 193

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

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	398
242014750	371	conserved hypothetical protein [Pediculu	0.635	0.681	0.734	4e-99
156538565	395	PREDICTED: hypothetical protein LOC10012	0.645	0.650	0.762	1e-98
383856328	316	PREDICTED: RNA-binding protein Musashi h	0.550	0.693	0.827	5e-97
340730010	390	PREDICTED: DAZ-associated protein 1-like	0.550	0.561	0.822	8e-97
189234173	373	PREDICTED: similar to heterogeneous nucl	0.600	0.640	0.768	2e-96
270002456	358	hypothetical protein TcasGA2_TC004519 [T	0.600	0.667	0.768	3e-96
198453793	643	GA27393 [Drosophila pseudoobscura pseudo	0.515	0.318	0.800	9e-96
347966951	556	AGAP001993-PA [Anopheles gambiae str. PE	0.525	0.375	0.816	2e-95
157112076	482	heterogeneous nuclear ribonucleoprotein	0.527	0.435	0.811	1e-94
194741664	634	GF17697 [Drosophila ananassae] gi|190626	0.502	0.315	0.810	1e-93

>gi|242014750|ref|XP_002428048.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212512567|gb|EEB15310.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  367 bits (943), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 188/256 (73%), Positives = 207/256 (80%), Gaps = 3/256 (1%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
           NG  SG+ G S+P  D   + KLFVGGLSWQTSSEKLR+YFGMFG +TDVLIMKDP+TQR
Sbjct: 39  NGTGSGNEGSSSPGADSTAAGKLFVGGLSWQTSSEKLRQYFGMFGNITDVLIMKDPVTQR 98

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDT 261
           SRGFGFITF EP +VE VLKVP+HTLDGKKIDPKHATPK R K   +TKKIFVGGVSQDT
Sbjct: 99  SRGFGFITFEEPSSVENVLKVPVHTLDGKKIDPKHATPKGRGKTNGKTKKIFVGGVSQDT 158

Query: 262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVE 321
           S++EVK YFSQFGKVEE VMLMDQQTKRHRGFGFVTFENEE VD +CEIHFH IKNKKVE
Sbjct: 159 SSDEVKVYFSQFGKVEEAVMLMDQQTKRHRGFGFVTFENEETVDRVCEIHFHNIKNKKVE 218

Query: 322 CKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQL--AALQSQAQAQVQAAAAA 379
           CKKA PKE V   LL GKR+++GPLG+RM  P P+T ATQL     Q+        AAAA
Sbjct: 219 CKKAMPKEVVAGTLL-GKRMVVGPLGVRMGIPTPVTQATQLVAVQAQAAHVQAAAVAAAA 277

Query: 380 VAAQNAAAVANYGKIF 395
             AQNAAAV+NYGKIF
Sbjct: 278 AQAQNAAAVSNYGKIF 293

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156538565|ref|XP_001607438.1| PREDICTED: hypothetical protein LOC100123736 [Nasonia vitripennis]

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 202/265 (76%), Positives = 216/265 (81%), Gaps = 8/265 (3%)

Query: 138 LVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP 197
           LV +NG  S  SGRSTP G DP   KLFVGGLSWQTSSEKLREYFGMFG VTDVLIMKDP
Sbjct: 31  LVPINGSHSSSSGRSTPNGGDPAPGKLFVGGLSWQTSSEKLREYFGMFGTVTDVLIMKDP 90

Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGV 257
           +TQRSRGFGFITFAEP +V+KVLK PIHTLDGKKIDPKHATPKNR K  NRTKKIFVGGV
Sbjct: 91  VTQRSRGFGFITFAEPGSVDKVLKCPIHTLDGKKIDPKHATPKNRAKQANRTKKIFVGGV 150

Query: 258 SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKN 317
           SQDTS+EEVKAYF+QFGKVEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKN
Sbjct: 151 SQDTSSEEVKAYFNQFGKVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKN 210

Query: 318 KKVECKKAQPKEAVQ-ANLLVGKRVILGPLGLRMAAPAPITP------ATQLAALQSQAQ 370
           KKVECKKAQPKEAVQ   L +GKRV+LG LG+R+ AP P  P      A+QL A      
Sbjct: 211 KKVECKKAQPKEAVQPGALALGKRVVLGALGVRL-APQPAMPVSGAAVASQLVAQAQAQA 269

Query: 371 AQVQAAAAAVAAQNAAAVANYGKIF 395
               AAAAA AAQ   AVA YGK+F
Sbjct: 270 QVQAAAAAAAAAQVQNAVAGYGKLF 294

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383856328|ref|XP_003703661.1| PREDICTED: RNA-binding protein Musashi homolog Rbp6-like [Megachile rotundata]

 Score =  360 bits (925), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 182/220 (82%), Positives = 195/220 (88%), Gaps = 1/220 (0%)

Query: 138 LVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP 197
           LV +NG  SG SGRSTP G DP   KLFVGGLSWQTSSEKLREYFGMFG VTDVLIMKDP
Sbjct: 16  LVPINGSHSGSSGRSTPNGGDPAPGKLFVGGLSWQTSSEKLREYFGMFGTVTDVLIMKDP 75

Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGV 257
           +TQRSRGFGFITFAEP +V+KVLK PIHTLDGKKIDPKHATPKNR K  NRTKKIFVGGV
Sbjct: 76  VTQRSRGFGFITFAEPGSVDKVLKCPIHTLDGKKIDPKHATPKNRAKQANRTKKIFVGGV 135

Query: 258 SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKN 317
           SQDTS+EEVKAYF+QFGKVEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKN
Sbjct: 136 SQDTSSEEVKAYFNQFGKVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKN 195

Query: 318 KKVECKKAQPKEAV-QANLLVGKRVILGPLGLRMAAPAPI 356
           KKVECKKAQPKEAV Q  L +GKRV+LG LG+R+A   P+
Sbjct: 196 KKVECKKAQPKEAVQQGALALGKRVVLGALGVRLAPQPPL 235

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340730010|ref|XP_003403285.1| PREDICTED: DAZ-associated protein 1-like [Bombus terrestris]

 Score =  360 bits (923), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 181/220 (82%), Positives = 195/220 (88%), Gaps = 1/220 (0%)

Query: 138 LVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP 197
           LV +NG  SG SGRSTP G DP   KLFVGGLSWQTSSEKLREYFGMFG VTDVLIMKDP
Sbjct: 37  LVPINGSHSGSSGRSTPNGGDPAPGKLFVGGLSWQTSSEKLREYFGMFGTVTDVLIMKDP 96

Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGV 257
           +TQRSRGFGFITFAEP +V+KVLK PIHTLDGKKIDPKHATPKNR K  NRTKKIFVGGV
Sbjct: 97  VTQRSRGFGFITFAEPGSVDKVLKCPIHTLDGKKIDPKHATPKNRAKQANRTKKIFVGGV 156

Query: 258 SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKN 317
           SQDTS++EVKAYF+QFGKVEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKN
Sbjct: 157 SQDTSSDEVKAYFNQFGKVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKN 216

Query: 318 KKVECKKAQPKEAVQ-ANLLVGKRVILGPLGLRMAAPAPI 356
           KKVECKKAQPKEAVQ   L +GKRV+LG LG+R+A   P+
Sbjct: 217 KKVECKKAQPKEAVQPGALTLGKRVVLGALGVRLAPQPPL 256

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234173|ref|XP_968418.2| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein [Tribolium castaneum]

 Score =  358 bits (920), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 186/242 (76%), Positives = 203/242 (83%), Gaps = 3/242 (1%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +DP   KLFVGGLSWQTSSEKLREYFGMFG VTDVLIMKDP+TQRSRGFGFITF+EP +V
Sbjct: 51  NDPAPGKLFVGGLSWQTSSEKLREYFGMFGNVTDVLIMKDPVTQRSRGFGFITFSEPSSV 110

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV 276
           + VLKVPIHTLDGKKIDPKHATPKNRPK  N+TKKIFVGGVSQDTSA+EVKAYFSQFGKV
Sbjct: 111 DNVLKVPIHTLDGKKIDPKHATPKNRPKQPNKTKKIFVGGVSQDTSADEVKAYFSQFGKV 170

Query: 277 EETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANL- 335
           EETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKNKKVECKKAQPKEAVQA+  
Sbjct: 171 EETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKNKKVECKKAQPKEAVQASAQ 230

Query: 336 LVGKRVILGPLGLRMAAP--APITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGK 393
           L+GKR++L  LG+RMA P    I  AT   A+         AA AA A    AAVA+YGK
Sbjct: 231 LLGKRLMLSGLGMRMATPTAGAIAAATNPLAVVQAQAHVQAAAVAAAAQAQTAAVASYGK 290

Query: 394 IF 395
           +F
Sbjct: 291 LF 292

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270002456|gb|EEZ98903.1| hypothetical protein TcasGA2_TC004519 [Tribolium castaneum]

 Score =  358 bits (919), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 186/242 (76%), Positives = 203/242 (83%), Gaps = 3/242 (1%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +DP   KLFVGGLSWQTSSEKLREYFGMFG VTDVLIMKDP+TQRSRGFGFITF+EP +V
Sbjct: 36  NDPAPGKLFVGGLSWQTSSEKLREYFGMFGNVTDVLIMKDPVTQRSRGFGFITFSEPSSV 95

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV 276
           + VLKVPIHTLDGKKIDPKHATPKNRPK  N+TKKIFVGGVSQDTSA+EVKAYFSQFGKV
Sbjct: 96  DNVLKVPIHTLDGKKIDPKHATPKNRPKQPNKTKKIFVGGVSQDTSADEVKAYFSQFGKV 155

Query: 277 EETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANL- 335
           EETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKNKKVECKKAQPKEAVQA+  
Sbjct: 156 EETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKNKKVECKKAQPKEAVQASAQ 215

Query: 336 LVGKRVILGPLGLRMAAP--APITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGK 393
           L+GKR++L  LG+RMA P    I  AT   A+         AA AA A    AAVA+YGK
Sbjct: 216 LLGKRLMLSGLGMRMATPTAGAIAAATNPLAVVQAQAHVQAAAVAAAAQAQTAAVASYGK 275

Query: 394 IF 395
           +F
Sbjct: 276 LF 277

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198453793|ref|XP_002137742.1| GA27393 [Drosophila pseudoobscura pseudoobscura] gi|198132515|gb|EDY68300.1| GA27393 [Drosophila pseudoobscura pseudoobscura]

 Score =  356 bits (914), Expect = 9e-96,   Method: Compositional matrix adjust.
 Identities = 169/211 (80%), Positives = 186/211 (88%), Gaps = 6/211 (2%)

Query: 146 SGDSGRSTPT-----GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
           SG SGRSTP+     G DP   KLFVGGLSWQTSS+KL+EYF MFG VTDVLIMKDP+TQ
Sbjct: 189 SGSSGRSTPSLTGGSGSDPAPGKLFVGGLSWQTSSDKLKEYFNMFGTVTDVLIMKDPVTQ 248

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQD 260
           RSRGFGFITF +P TVEKVLKVPIHTLDGKKIDPKHATPKNRP+  N+TKKIFVGGVSQD
Sbjct: 249 RSRGFGFITFQDPCTVEKVLKVPIHTLDGKKIDPKHATPKNRPRQANKTKKIFVGGVSQD 308

Query: 261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKV 320
           TSAEEVKAYF+QFG VEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKNKKV
Sbjct: 309 TSAEEVKAYFAQFGPVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKNKKV 368

Query: 321 ECKKAQPKEAVQ-ANLLVGKRVILGPLGLRM 350
           ECKKAQPKE+V  A  L+ KR++LG LG+++
Sbjct: 369 ECKKAQPKESVTPAAQLLQKRIMLGSLGVQL 399

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347966951|ref|XP_321067.5| AGAP001993-PA [Anopheles gambiae str. PEST] gi|333469826|gb|EAA01260.6| AGAP001993-PA [Anopheles gambiae str. PEST]

 Score =  355 bits (911), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 174/213 (81%), Positives = 185/213 (86%), Gaps = 4/213 (1%)

Query: 142 NGKSSGDSGRSTPT-GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
           N  +   SGRSTP  G DP   KLFVGGLSWQTSSEKL EYFGMFG VTDVLIMKDP+TQ
Sbjct: 161 NASNGSSSGRSTPNNGSDPAPGKLFVGGLSWQTSSEKLSEYFGMFGTVTDVLIMKDPVTQ 220

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKI-GNRTKKIFVGGVSQ 259
           RSRGFGFITF EP +V+KVL+VPIHTLDGKKIDPKHATPKNRPK   N+TKKIFVGGVSQ
Sbjct: 221 RSRGFGFITFQEPNSVDKVLQVPIHTLDGKKIDPKHATPKNRPKTQSNKTKKIFVGGVSQ 280

Query: 260 DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKK 319
           DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKNKK
Sbjct: 281 DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKNKK 340

Query: 320 VECKKAQPKEAV--QANLLVGKRVILGPLGLRM 350
           VECKKAQPKEAV   A  L+ KR+ILG LG+ M
Sbjct: 341 VECKKAQPKEAVAPTAQQLLQKRIILGNLGVPM 373

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157112076|ref|XP_001651782.1| heterogeneous nuclear ribonucleoprotein [Aedes aegypti] gi|108878175|gb|EAT42400.1| AAEL006057-PA [Aedes aegypti]

 Score =  353 bits (905), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 176/217 (81%), Positives = 187/217 (86%), Gaps = 7/217 (3%)

Query: 141 VNGKSSGDSGRSTP-TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT 199
            NG SSG   RSTP +  DP   KLFVGGLSWQTSSEKL EYFGMFG VTDVLIMKDPIT
Sbjct: 83  TNGSSSG---RSTPNSSSDPAPGKLFVGGLSWQTSSEKLSEYFGMFGKVTDVLIMKDPIT 139

Query: 200 QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKI-GNRTKKIFVGGVS 258
           QRSRGFGFITF EP +V+KVLKVPIHTLDGKKIDPKHATPKNRPK   N+TKKIFVGGVS
Sbjct: 140 QRSRGFGFITFQEPNSVDKVLKVPIHTLDGKKIDPKHATPKNRPKTQSNKTKKIFVGGVS 199

Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNK 318
           QDTSAEEV+ YFSQFGKV+ETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKNK
Sbjct: 200 QDTSAEEVRQYFSQFGKVDETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKNK 259

Query: 319 KVECKKAQPKEAV--QANLLVGKRVILGPLGLRMAAP 353
           KVECKKAQPKEAV   A  L+ KR+ILG LGL +A P
Sbjct: 260 KVECKKAQPKEAVTPTAQQLLQKRIILGNLGLPIATP 296

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194741664|ref|XP_001953309.1| GF17697 [Drosophila ananassae] gi|190626368|gb|EDV41892.1| GF17697 [Drosophila ananassae]

 Score =  349 bits (896), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 167/206 (81%), Positives = 182/206 (88%), Gaps = 6/206 (2%)

Query: 151 RSTPT-----GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
           RSTP+     G DP   KLFVGGLSWQTSS+KL+EYF MFG VTDVLIMKDP+TQRSRGF
Sbjct: 189 RSTPSLTGGSGSDPAPGKLFVGGLSWQTSSDKLKEYFNMFGTVTDVLIMKDPVTQRSRGF 248

Query: 206 GFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEE 265
           GFITF EP TV+KVLKVPIHTLDGKKIDPKHATPKNRP+  N+TKKIFVGGVSQDTSAEE
Sbjct: 249 GFITFQEPCTVQKVLKVPIHTLDGKKIDPKHATPKNRPRQANKTKKIFVGGVSQDTSAEE 308

Query: 266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA 325
           VKAYFSQFG VEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIHFH IKNKKVECKKA
Sbjct: 309 VKAYFSQFGPVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIHFHTIKNKKVECKKA 368

Query: 326 QPKEAVQ-ANLLVGKRVILGPLGLRM 350
           QPKEAV  A  L+ KR++LG LG+++
Sbjct: 369 QPKEAVTPAAQLLQKRIMLGTLGVQL 394

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	398
FB|FBgn0011666	634	msi "musashi" [Drosophila mela	0.552	0.347	0.770	3.6e-89
UNIPROTKB|Q96DH6	328	MSI2 "RNA-binding protein Musa	0.469	0.570	0.596	1e-59
MGI|MGI:1923876	346	Msi2 "musashi RNA-binding prot	0.469	0.540	0.596	1.3e-59
FB|FBgn0260943	369	Rbp6 "RNA-binding protein 6" [	0.444	0.479	0.607	2.7e-59
ZFIN|ZDB-GENE-040426-1268	408	msi2b "musashi homolog 2b (Dro	0.464	0.453	0.585	8.4e-58
UNIPROTKB|B4DHE8	324	MSI2 "RNA-binding protein Musa	0.422	0.518	0.621	5.9e-57
ZFIN|ZDB-GENE-030826-25	388	msi2a "musashi homolog 2a (Dro	0.454	0.466	0.592	5.9e-57
UNIPROTKB|O43347	362	MSI1 "RNA-binding protein Musa	0.494	0.544	0.552	2e-56
MGI|MGI:107376	362	Msi1 "musashi RNA-binding prot	0.494	0.544	0.552	2.5e-56
RGD|628778	362	Msi1 "musashi RNA-binding prot	0.494	0.544	0.552	2.5e-56

FB|FBgn0011666 msi "musashi" [Drosophila melanogaster (taxid:7227)]

 Score = 890 (318.4 bits), Expect = 3.6e-89, P = 3.6e-89
 Identities = 175/227 (77%), Positives = 191/227 (84%)

Query:   137 QLVLVNGKSSGDSGRSTPT-----GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDV 191
             Q  +     SG SGRSTP+     G DP   KLFVGGLSWQTSS+KL+EYF MFG VTDV
Sbjct:   173 QAAMGGSNKSGSSGRSTPSLSGGSGSDPAPGKLFVGGLSWQTSSDKLKEYFNMFGTVTDV 232

Query:   192 LIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
             LIMKDP+TQRSRGFGFITF EP TVEKVLKVPIHTLDGKKIDPKHATPKNRP+  N+TKK
Sbjct:   233 LIMKDPVTQRSRGFGFITFQEPCTVEKVLKVPIHTLDGKKIDPKHATPKNRPRQANKTKK 292

Query:   252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
             IFVGGVSQDTSAEEVKAYFSQFG VEETVMLMDQQTKRHRGFGFVTFENE+VVD +CEIH
Sbjct:   293 IFVGGVSQDTSAEEVKAYFSQFGPVEETVMLMDQQTKRHRGFGFVTFENEDVVDRVCEIH 352

Query:   312 FHMIKNKKVECKKAQPKEAVQ-ANLLVGKRVILGPLGLRM-AAPAPI 356
             FH IKNKKVECKKAQPKEAV  A  L+ KR++LG LG+++  AP  +
Sbjct:   353 FHTIKNKKVECKKAQPKEAVTPAAQLLQKRIMLGTLGVQLPTAPGQL 399

GO:0005634 "nucleus" evidence=IDA

GO:0022416 "chaeta development" evidence=IMP

GO:0003723 "RNA binding" evidence=ISM

GO:0003729 "mRNA binding" evidence=ISS;NAS;TAS

GO:0006397 "mRNA processing" evidence=ISS

GO:0017148 "negative regulation of translation" evidence=IMP;TAS

GO:0006417 "regulation of translation" evidence=TAS

GO:0045182 "translation regulator activity" evidence=TAS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001709 "cell fate determination" evidence=TAS

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

GO:0019827 "stem cell maintenance" evidence=IMP

GO:0042078 "germ-line stem cell division" evidence=IMP

GO:0071456 "cellular response to hypoxia" evidence=IMP

UNIPROTKB|Q96DH6 MSI2 "RNA-binding protein Musashi homolog 2" [Homo sapiens (taxid:9606)]

 Score = 612 (220.5 bits), Expect = 1.0e-59, P = 1.0e-59
 Identities = 114/191 (59%), Positives = 145/191 (75%)

Query:   142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
             NG S G SG +  +  DP   K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+R
Sbjct:     4 NG-SQGTSGSANDSQHDP--GKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKR 60

Query:   202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQD 260
             SRGFGF+TFA+P +V+KVL  P H LD K IDPK A P+  +PK+  RTKKIFVGG+S +
Sbjct:    61 SRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSAN 120

Query:   261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKV 320
             T  E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +CEIHFH I NK V
Sbjct:   121 TVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMV 180

Query:   321 ECKKAQPKEAV 331
             ECKKAQPKE +
Sbjct:   181 ECKKAQPKEVM 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0048864 "stem cell development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

MGI|MGI:1923876 Msi2 "musashi RNA-binding protein 2" [Mus musculus (taxid:10090)]

 Score = 611 (220.1 bits), Expect = 1.3e-59, P = 1.3e-59
 Identities = 114/191 (59%), Positives = 145/191 (75%)

Query:   142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
             NG S G SG +  +  DP   K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+R
Sbjct:     4 NG-SPGTSGSANDSQHDP--GKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKR 60

Query:   202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQD 260
             SRGFGF+TFA+P +V+KVL  P H LD K IDPK A P+  +PK+  RTKKIFVGG+S +
Sbjct:    61 SRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSAN 120

Query:   261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKV 320
             T  E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +CEIHFH I NK V
Sbjct:   121 TVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMV 180

Query:   321 ECKKAQPKEAV 331
             ECKKAQPKE +
Sbjct:   181 ECKKAQPKEVM 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003727 "single-stranded RNA binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005844 "polysome" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0048864 "stem cell development" evidence=IMP

FB|FBgn0260943 Rbp6 "RNA-binding protein 6" [Drosophila melanogaster (taxid:7227)]

 Score = 608 (219.1 bits), Expect = 2.7e-59, P = 2.7e-59
 Identities = 110/181 (60%), Positives = 144/181 (79%)

Query:   157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
             +DP   K+F+GGLSWQTS E LR+YFG +G +++ ++MKDP T+RSRGFGF+TF++P +V
Sbjct:    26 NDP--GKMFIGGLSWQTSPESLRDYFGRYGDISEAMVMKDPTTRRSRGFGFVTFSDPNSV 83

Query:   217 EKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK 275
             +KVL    H LDGKK+DPK A P+   PK+  RTKKIFVGG+S  T+ E+VK+YF QFG 
Sbjct:    84 DKVLTQGTHELDGKKVDPKVAFPRRAHPKMVTRTKKIFVGGLSAPTTLEDVKSYFEQFGP 143

Query:   276 VEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAV-QAN 334
             +E+ +++ D+QT RHRGFGFVTF++E+VVD +CEIHFH I NK VECKKAQPKE +  AN
Sbjct:   144 IEDAMLMFDKQTNRHRGFGFVTFQSEDVVDKVCEIHFHEINNKMVECKKAQPKEVMLPAN 203

Query:   335 L 335
             L
Sbjct:   204 L 204

GO:0003729 "mRNA binding" evidence=NAS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1268 msi2b "musashi homolog 2b (Drosophila)" [Danio rerio (taxid:7955)]

 Score = 594 (214.2 bits), Expect = 8.4e-58, P = 8.4e-58
 Identities = 110/188 (58%), Positives = 140/188 (74%)

Query:   145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
             S   SG    +  DP   K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+RSRG
Sbjct:     6 SQATSGSPNDSQHDP--GKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRG 63

Query:   205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSA 263
             FGF+TFA+  +V+KVL  P H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T  
Sbjct:    64 FGFVTFADAASVDKVLAQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSANTVV 123

Query:   264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK 323
             E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +CEIHFH I NK VECK
Sbjct:   124 EDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECK 183

Query:   324 KAQPKEAV 331
             KAQPKE +
Sbjct:   184 KAQPKEVM 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|B4DHE8 MSI2 "RNA-binding protein Musashi homolog 2" [Homo sapiens (taxid:9606)]

 Score = 586 (211.3 bits), Expect = 5.9e-57, P = 5.9e-57
 Identities = 105/169 (62%), Positives = 134/169 (79%)

Query:   164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
             +F+GGLSWQTS + LR+YF  FG + + ++M+DP T+RSRGFGF+TFA+P +V+KVL  P
Sbjct:     1 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQP 60

Query:   224 IHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML 282
              H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T  E+VK YF QFGKVE+ +++
Sbjct:    61 HHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLM 120

Query:   283 MDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAV 331
              D+ T RHRGFGFVTFENE+VV+ +CEIHFH I NK VECKKAQPKE +
Sbjct:   121 FDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKKAQPKEVM 169

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-030826-25 msi2a "musashi homolog 2a (Drosophila)" [Danio rerio (taxid:7955)]

 Score = 586 (211.3 bits), Expect = 5.9e-57, P = 5.9e-57
 Identities = 109/184 (59%), Positives = 138/184 (75%)

Query:   149 SGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
             SG    +  DP   K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+RSRGFGFI
Sbjct:    10 SGSLNDSQHDP--GKMFIGGLSWQTSPDSLRDYFCKFGEIRECMVMRDPTTKRSRGFGFI 67

Query:   209 TFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVK 267
             TFA+  +V+KVL  P H LD K IDPK A P+  +PK+  RTKKIFVGG+S  T  E+VK
Sbjct:    68 TFADVSSVDKVLAQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSASTVVEDVK 127

Query:   268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP 327
              YF QFGKVE+ +++ D+ T RHRGFGFVTFENE++V+ +CEIHFH I NK VECKKAQP
Sbjct:   128 QYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDIVEKVCEIHFHEINNKMVECKKAQP 187

Query:   328 KEAV 331
             KE +
Sbjct:   188 KEVM 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|O43347 MSI1 "RNA-binding protein Musashi homolog 1" [Homo sapiens (taxid:9606)]

 Score = 581 (209.6 bits), Expect = 2.0e-56, P = 2.0e-56
 Identities = 111/201 (55%), Positives = 145/201 (72%)

Query:   150 GRSTPTGD-DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
             G ++P    DP   K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+
Sbjct:     9 GLASPDSPHDP--CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 66

Query:   209 TFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVK 267
             TF +   V+KVL    H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T+ E+VK
Sbjct:    67 TFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVK 126

Query:   268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP 327
              YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEIHFH I NK VECKKAQP
Sbjct:   127 QYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQP 186

Query:   328 KEAVQANLLVGKRVILGPLGL 348
             KE +        R  + P G+
Sbjct:   187 KEVMSPTGSARGRSRVMPYGM 207

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0009725 "response to hormone stimulus" evidence=IEA

GO:0030855 "epithelial cell differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=TAS

GO:0007399 "nervous system development" evidence=TAS

MGI|MGI:107376 Msi1 "musashi RNA-binding protein 1" [Mus musculus (taxid:10090)]

 Score = 580 (209.2 bits), Expect = 2.5e-56, P = 2.5e-56
 Identities = 111/201 (55%), Positives = 145/201 (72%)

Query:   150 GRSTPTGD-DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
             G ++P    DP   K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+
Sbjct:     9 GLASPDSPHDP--CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 66

Query:   209 TFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVK 267
             TF +   V+KVL    H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T+ E+VK
Sbjct:    67 TFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVK 126

Query:   268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP 327
              YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEIHFH I NK VECKKAQP
Sbjct:   127 HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQP 186

Query:   328 KEAVQANLLVGKRVILGPLGL 348
             KE +        R  + P G+
Sbjct:   187 KEVMSPTGSARGRSRVMPYGM 207

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003727 "single-stranded RNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005844 "polysome" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009725 "response to hormone stimulus" evidence=ISO

RGD|628778 Msi1 "musashi RNA-binding protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 580 (209.2 bits), Expect = 2.5e-56, P = 2.5e-56
 Identities = 111/201 (55%), Positives = 145/201 (72%)

Query:   150 GRSTPTGD-DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
             G ++P    DP   K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+
Sbjct:     9 GLASPDSPHDP--CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 66

Query:   209 TFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDTSAEEVK 267
             TF +   V+KVL    H LD K IDPK A P+  +PK+  RTKKIFVGG+S +T+ E+VK
Sbjct:    67 TFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVK 126

Query:   268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP 327
              YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEIHFH I NK VECKKAQP
Sbjct:   127 HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQP 186

Query:   328 KEAVQANLLVGKRVILGPLGL 348
             KE +        R  + P G+
Sbjct:   187 KEVMSPTGSARGRSRVMPYGM 207

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=NAS

GO:0003727 "single-stranded RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0005844 "polysome" evidence=IEA;ISO

GO:0008266 "poly(U) RNA binding" evidence=IEA;ISO

GO:0009725 "response to hormone stimulus" evidence=IMP

GO:0030855 "epithelial cell differentiation" evidence=IEP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8K3P4	MSI1H_RAT	No assigned EC number	0.5691	0.4698	0.5165	yes	N/A
Q920Q6	MSI2H_MOUSE	No assigned EC number	0.5957	0.4648	0.5346	yes	N/A
Q96DH6	MSI2H_HUMAN	No assigned EC number	0.5957	0.4648	0.5640	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	398
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	9e-43
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-40
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	8e-38
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	6e-35
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	6e-34
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-32
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	4e-30
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-29
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-29
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-27
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-27
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-27
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-27
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-27
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-25
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-25
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-25
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	7e-24
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-23
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-23
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-23
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-22
smart00360	73	smart00360, RRM, RNA recognition motif	5e-22
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	7e-22
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	1e-21
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-21
smart00360	73	smart00360, RRM, RNA recognition motif	5e-21
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	9e-21
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-20
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-19
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-19
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-19
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	6e-19
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	9e-19
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-18
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-18
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	5e-18
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	6e-18
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-17
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-17
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-17
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-17
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	4e-17
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	5e-17
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	9e-17
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-16
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-16
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-16
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-16
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	3e-16
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	4e-16
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	4e-16
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	6e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-15
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-15
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-15
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-15
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	3e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-15
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-15
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-15
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-15
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-15
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	9e-15
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-14
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-14
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-14
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-14
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-14
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	5e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-14
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	6e-14
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	6e-14
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-14
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	7e-14
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	7e-14
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-14
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-14
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	9e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-13
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-13
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	5e-13
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-13
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-12
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-12
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-12
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	6e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-12
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	8e-12
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	9e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	9e-12
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-11
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	7e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	9e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-10
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-10
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-10
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-09
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-09
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-09
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-09
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-09
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	8e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	9e-09
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-08
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-08
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	4e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-08
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-08
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	8e-08
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-07
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	6e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	7e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	7e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	8e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-06
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	4e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-06
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	5e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	5e-06
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	5e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	6e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	6e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	6e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-06
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	8e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	9e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	9e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	1e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	1e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	3e-05
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	3e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-05
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	3e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	4e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-05
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	4e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	5e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	6e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	6e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	7e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	7e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	8e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	8e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	8e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	9e-05
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	9e-05
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	9e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	1e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-04
cd12623	91	cd12623, RRM_PPARGC1A, RNA recognition motif in pe	1e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	3e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	3e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	3e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	3e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-04
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	3e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	4e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	4e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	4e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	4e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	4e-04
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	4e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	5e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	6e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-04
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	7e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	7e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	8e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	8e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	9e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.001
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.001
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.001
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.001
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.001
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.001
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.001
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.001
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.002
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.002
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.002
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.002
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.002
cd12624	91	cd12624, RRM_PRC, RNA recognition motif in peroxis	0.002
cd12301	74	cd12301, RRM1_2_PAR10_like, RNA recognition motif	0.002
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.002
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.002
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.002
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	0.002
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.002
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.003
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.003
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	0.003
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	0.003
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.003
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.003
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.003
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.003
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.003
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.004
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.004
cd12505	75	cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-	0.004

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

 Score =  143 bits (363), Expect = 9e-43
 Identities = 51/74 (68%), Positives = 64/74 (86%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S +T+ ++VK YFSQFGKVE+ +++ D+QT RHRGFGFVTFE+E+VVD +CEI
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 311 HFHMIKNKKVECKK 324
           HFH I NK VECKK
Sbjct: 61  HFHEINNKMVECKK 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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score =  136 bits (346), Expect = 3e-40
 Identities = 47/72 (65%), Positives = 57/72 (79%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LF+GGLSW T+ E LREYF  +G V D +IMKDPIT RSRGFGF+TFA+P +V+KVL   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 224 IHTLDGKKIDPK 235
            H LDG++IDPK
Sbjct: 61  PHVLDGREIDPK 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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score =  131 bits (330), Expect = 8e-38
 Identities = 45/74 (60%), Positives = 60/74 (81%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +F+GGLSWQT++E LREYF  FG + + ++M+DP T+RSRGFGF+TF++P +V+KVL   
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 224 IHTLDGKKIDPKHA 237
            H LDGKKIDPK 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 =  123 bits (309), Expect = 6e-35
 Identities = 54/78 (69%), Positives = 65/78 (83%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
           RTKKIFVGG+S +T  E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +
Sbjct: 2   RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61

Query: 308 CEIHFHMIKNKKVECKKA 325
           CEIHFH I NK VECKKA
Sbjct: 62  CEIHFHEINNKMVECKKA 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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score =  120 bits (302), Expect = 6e-34
 Identities = 47/74 (63%), Positives = 62/74 (83%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S +T+ E+VK YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEI
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 311 HFHMIKNKKVECKK 324
           HFH I NK VECKK
Sbjct: 61  HFHEINNKMVECKK 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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score =  117 bits (294), Expect = 2e-32
 Identities = 43/80 (53%), Positives = 58/80 (72%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
           RTKKIFVGG+  + +  +++ YFSQFG V E V++ D + KR RGFGF+TFE+E+ VD +
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 308 CEIHFHMIKNKKVECKKAQP 327
              HFH I  KKVE K+A+P
Sbjct: 61  VNEHFHDINGKKVEVKRAEP 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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score =  110 bits (277), Expect = 4e-30
 Identities = 46/78 (58%), Positives = 54/78 (69%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVGGLSW+T+ E LR YF  +G V D +IMKD  T RSRGFGF+ F +P  V  VL  
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 223 PIHTLDGKKIDPKHATPK 240
             HTLDG+ IDPK  TP+
Sbjct: 61  GPHTLDGRTIDPKPCTPR 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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score =  107 bits (270), Expect = 5e-29
 Identities = 37/78 (47%), Positives = 57/78 (73%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ + L+ YF  +G +TD ++MKDP T+RSRGFGF+TFA    V+  +  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 223 PIHTLDGKKIDPKHATPK 240
             H +DG++++PK A P+
Sbjct: 61  RPHKVDGREVEPKRAVPR 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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score =  107 bits (268), Expect = 8e-29
 Identities = 44/77 (57%), Positives = 59/77 (76%), Gaps = 1/77 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +F+GGL+W+T+ + LREYFG FG VTD  +M+D  T RSRGFGF+TF +P++V +V+K  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 224 IHTLDGKKIDPKHATPK 240
            H LDGK IDPK A P+
Sbjct: 61  -HILDGKIIDPKRAIPR 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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score =  104 bits (260), Expect = 1e-27
 Identities = 45/75 (60%), Positives = 59/75 (78%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSWQTS + LR+YF  FG + + ++M+DP T+RSRGFGF+TFA+P +V+KVL  
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 223 PIHTLDGKKIDPKHA 237
           P H LD K IDPK A
Sbjct: 61  PHHELDSKTIDPKVA 75

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

 Score =  103 bits (258), Expect = 2e-27
 Identities = 38/75 (50%), Positives = 54/75 (72%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S +T+ E+++ YF +FG + E  + MD++T + RGF F+TF++EE V  I E 
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 311 HFHMIKNKKVECKKA 325
            FH+I  KKVE KKA
Sbjct: 61  QFHVIGGKKVEVKKA 75

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

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

 Score =  103 bits (257), Expect = 3e-27
 Identities = 42/74 (56%), Positives = 51/74 (68%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FVGGLSW T+ + L+EYF  FG V D  I  DP+T RSRGFGF+ F +  +VEKVL   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 224 IHTLDGKKIDPKHA 237
            H LDG+ IDPK A
Sbjct: 61  EHKLDGRVIDPKRA 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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score =  102 bits (255), Expect = 4e-27
 Identities = 45/75 (60%), Positives = 53/75 (70%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLSW TS + L++YF  FG VTD  I  DP T RSRGFGFI F +  +VEKVL+ 
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 223 PIHTLDGKKIDPKHA 237
             H LDG+ IDPK A
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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score =  102 bits (255), Expect = 4e-27
 Identities = 46/75 (61%), Positives = 57/75 (76%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 223 PIHTLDGKKIDPKHA 237
             H LD K IDPK 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 98.2 bits (245), Expect = 2e-25
 Identities = 36/75 (48%), Positives = 48/75 (64%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+  D + EE K YFSQFGKV +  ++ D  T R RGFGFVTF++E  V+ +   
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 311 HFHMIKNKKVECKKA 325
               +  K+VE K+A
Sbjct: 61  GMLELGGKQVEVKRA 75

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

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

 Score = 97.8 bits (243), Expect = 2e-25
 Identities = 42/75 (56%), Positives = 52/75 (69%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSW TS + L EY   FG V D  I  DP+T RSRGFGF+ F +  +V+KVL++
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 223 PIHTLDGKKIDPKHA 237
             H LDGK IDPK A
Sbjct: 61  KEHKLDGKLIDPKRA 75

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

 Score = 96.5 bits (241), Expect = 6e-25
 Identities = 28/72 (38%), Positives = 48/72 (66%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +F+GG+S DT+ E ++ YFS++G+V + V++ D  T R RGFGFVTF +   VD +    
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 312 FHMIKNKKVECK 323
            H++  ++++ K
Sbjct: 61  PHVLDGREIDPK 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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 93.5 bits (232), Expect = 7e-24
 Identities = 40/74 (54%), Positives = 52/74 (70%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +F+GGLSW T+ + L++YF  FG V D  +  DPIT RSRGFGF+ F E E+V+KV+   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 224 IHTLDGKKIDPKHA 237
            H L+GK IDPK A
Sbjct: 61  EHKLNGKVIDPKRA 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 92.3 bits (230), Expect = 2e-23
 Identities = 31/73 (42%), Positives = 49/73 (67%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVGG+ +D + E+++ YFSQ+G VE   ++ D++T + RGF FVTF++ + VD I   
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 311 HFHMIKNKKVECK 323
            +H I   +VE K
Sbjct: 61  KYHTINGHRVEVK 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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 92.0 bits (229), Expect = 3e-23
 Identities = 35/79 (44%), Positives = 52/79 (65%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           + K+FVGGL    +   LR+YF  FG VT+V++M D   +R RGFGFITF   ++V++V+
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61

Query: 221 KVPIHTLDGKKIDPKHATP 239
               H ++GKK++ K A P
Sbjct: 62  NEHFHDINGKKVEVKRAEP 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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 91.7 bits (228), Expect = 3e-23
 Identities = 33/78 (42%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            L V GL W+T+ + L++YF  FG +  V + KDP T +S+GFGF+ FA+ E   KVL  
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 223 PIHTLDGKKIDPKHATPK 240
             H +DG+  D K    K
Sbjct: 61  R-HMIDGRWCDVKIPNSK 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 90.1 bits (224), Expect = 1e-22
 Identities = 34/75 (45%), Positives = 46/75 (61%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGL    + E+ +EYF  FG V D  +M+D  T RSRGFGF+TF     VE+V   
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 223 PIHTLDGKKIDPKHA 237
            +  L GK+++ K A
Sbjct: 61  GMLELGGKQVEVKRA 75

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

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

 Score = 88.4 bits (220), Expect = 5e-22
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
            LFVG L   T+ E+LRE F  FG V  V +++D  T +S+GF F+ F   E  EK L+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 222 VPIHTLDGKKID 233
           +    LDG+ + 
Sbjct: 61  LNGKELDGRPLK 72

Length = 73

>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 = 88.2 bits (219), Expect = 7e-22
 Identities = 36/75 (48%), Positives = 51/75 (68%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS +T+ EK+REYFG FG + ++ +  D  T + RGF FITF   E V+K+L+ 
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 223 PIHTLDGKKIDPKHA 237
             H + GKK++ K A
Sbjct: 61  QFHVIGGKKVEVKKA 75

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

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

 Score = 87.9 bits (217), Expect = 1e-21
 Identities = 35/78 (44%), Positives = 56/78 (71%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR Y+  +G +TD ++M+DP ++RSRGFGF+TF+    V+  +  
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

Query: 223 PIHTLDGKKIDPKHATPK 240
             HT+DG+ ++PK A  +
Sbjct: 64  RPHTIDGRVVEPKRAVAR 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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 87.4 bits (216), Expect = 2e-21
 Identities = 35/78 (44%), Positives = 56/78 (71%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T++  E V+  +  
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 223 PIHTLDGKKIDPKHATPK 240
             H +DG+ ++PK A  +
Sbjct: 64  RPHKVDGRVVEPKRAVSR 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|214636 smart00360, RRM, RNA recognition motif

 Score = 85.7 bits (213), Expect = 5e-21
 Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            +FVG +  DT+ EE++  FS+FGKVE   ++ D++T + +GF FV FE+EE  +   E 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 311 -HFHMIKNKKVEC 322
            +   +  + ++ 
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 85.5 bits (211), Expect = 9e-21
 Identities = 35/78 (44%), Positives = 57/78 (73%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ + LRE+F  +G +TD ++M+DP T+RSRGFGF+T++  E V+  +  
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 223 PIHTLDGKKIDPKHATPK 240
             H +DG+ ++PK A  +
Sbjct: 64  RPHKVDGRVVEPKRAVSR 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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 84.0 bits (208), Expect = 3e-20
 Identities = 31/73 (42%), Positives = 48/73 (65%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T+ + +++YF  FG V D ++M D  T R RGFGF+TF   + V+KV ++
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 223 PIHTLDGKKIDPK 235
             H ++ K ++ K
Sbjct: 61  HFHEINNKMVECK 73

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

 Score = 81.9 bits (203), Expect = 1e-19
 Identities = 31/73 (42%), Positives = 46/73 (63%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVGGL    + E LREYF  +G V  V I+ D  T + RGF F+TF + + V+K++  
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 223 PIHTLDGKKIDPK 235
             HT++G +++ K
Sbjct: 61  KYHTINGHRVEVK 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 81.9 bits (202), Expect = 1e-19
 Identities = 36/79 (45%), Positives = 50/79 (63%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVGG+  D    ++  +FSQFG VE+  ++ D+QT + RGFGFV F+N +  D    +
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 311 HFHMIKNKKVECKKAQPKE 329
            FH I   +VE KKA PKE
Sbjct: 61  KFHPINGHRVEVKKAVPKE 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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 80.2 bits (198), Expect = 6e-19
 Identities = 34/75 (45%), Positives = 53/75 (70%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVGGL+ +TS   LR +F  +G +T+ ++M DP T+RSRGFGFITF+  +  ++ ++ 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 223 PIHTLDGKKIDPKHA 237
             H++DG +I+ K A
Sbjct: 64  QPHSIDGNQIELKRA 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 80.4 bits (198), Expect = 6e-19
 Identities = 33/80 (41%), Positives = 50/80 (62%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           KKIFVGG+ +DT    ++ YF ++GK+E   ++ D+Q+ + RGF FVTF++ + VD I  
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60

Query: 310 IHFHMIKNKKVECKKAQPKE 329
             +H I     E KKA  K+
Sbjct: 61  QKYHTINGHNCEVKKALSKQ 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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 79.7 bits (197), Expect = 9e-19
 Identities = 33/78 (42%), Positives = 52/78 (66%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S +T+ + +K YFSQ+G++ + V++ D  TKR RGFGFVTF +   VD     
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 311 HFHMIKNKKVECKKAQPK 328
             H +  ++VE K+A P+
Sbjct: 61  RPHKVDGREVEPKRAVPR 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|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 = 79.2 bits (196), Expect = 1e-18
 Identities = 32/73 (43%), Positives = 47/73 (64%), Gaps = 4/73 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFV GLS +T+ ++L   F  FG V +VL+MKDP T  SRGFGF+TF   E  +  ++ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR- 61

Query: 223 PIHTLDGKKIDPK 235
               L+GK+++ +
Sbjct: 62  ---DLNGKELEGR 71

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

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            L+VG L +  + E L++ FG FG VT   ++ D  T RSRGFGF+     E        
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA--- 57

Query: 223 PIHTLDGKKID 233
            I  L+G    
Sbjct: 58  -IEKLNGTDFG 67

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

 Score = 77.7 bits (191), Expect = 5e-18
 Identities = 30/76 (39%), Positives = 47/76 (61%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           KKIFVGG+ +DT    ++ YF Q+GK+E   ++ D+ + + RGF FVTF++ + VD I  
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60

Query: 310 IHFHMIKNKKVECKKA 325
             +H +     E +KA
Sbjct: 61  QKYHTVNGHNCEVRKA 76

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

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

 Score = 77.4 bits (190), Expect = 6e-18
 Identities = 33/73 (45%), Positives = 48/73 (65%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T+ E +++YF  FG V D ++M D  T R RGFGF+TF   + VEKV ++
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 223 PIHTLDGKKIDPK 235
             H ++ K ++ K
Sbjct: 61  HFHEINNKMVECK 73

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

 Score = 75.8 bits (187), Expect = 2e-17
 Identities = 28/71 (39%), Positives = 42/71 (59%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVG L W   S++L+EYF  FG V    +  D  T  S+G+GF++F+  + +E  L+ 
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 223 PIHTLDGKKID 233
             H L+G K+ 
Sbjct: 61  QKHILEGNKLQ 71

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|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 = 76.0 bits (187), Expect = 2e-17
 Identities = 30/77 (38%), Positives = 52/77 (67%), Gaps = 1/77 (1%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV-EKVL 220
            KLF+GGLS+ T+ + L + F  +G +++V+++KD  TQRSRGFGF+TF  P+   + ++
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 221 KVPIHTLDGKKIDPKHA 237
            +   ++DG++I    A
Sbjct: 61  AMNGKSVDGRQIRVDQA 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 75.7 bits (187), Expect = 2e-17
 Identities = 29/69 (42%), Positives = 47/69 (68%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGL + T+ + LR+YF  FG + + +++ D  T +SRG+GF+TF + E+ E+  K 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 223 PIHTLDGKK 231
           P   +DG+K
Sbjct: 62  PNPIIDGRK 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 31/76 (40%), Positives = 50/76 (65%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
            KIFVGG+   T+ + ++ YFSQFG++EE V++ D+QT + RG+GFVTF+++E  +  C+
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 310 IHFHMIKNKKVECKKA 325
               +I  +K     A
Sbjct: 61  DPNPIIDGRKANVNLA 76

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

 Score = 75.2 bits (185), Expect = 4e-17
 Identities = 32/74 (43%), Positives = 50/74 (67%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +F+GG+S  T+AE ++ YFS+FG+++E +++ D  TKR RGFGFVTF +   VD +    
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 312 FHMIKNKKVECKKA 325
            H +  KK++ 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 = 75.1 bits (184), Expect = 5e-17
 Identities = 34/77 (44%), Positives = 49/77 (63%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           + K+FVGGLS  T  E +++YF  FG V D ++M D  T R RGFGF+TF   + VEKV 
Sbjct: 3   TKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVC 62

Query: 221 KVPIHTLDGKKIDPKHA 237
           ++  H ++ K ++ K A
Sbjct: 63  EIHFHEINNKMVECKKA 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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 73.9 bits (181), Expect = 9e-17
 Identities = 34/75 (45%), Positives = 48/75 (64%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVGG+S DT+ E++K YF  FG++E   + MD +T   RGF FVT+ +EE V  + E 
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 311 HFHMIKNKKVECKKA 325
            +H I + K E K A
Sbjct: 61  RYHQIGSGKCEIKVA 75

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

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

 Score = 73.4 bits (181), Expect = 1e-16
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 5/70 (7%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFVG L   T+ E L++ F  FG +  + I++D  T RS+GF F+ F + E  EK L+  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALE-- 57

Query: 224 IHTLDGKKID 233
              L+GK++ 
Sbjct: 58  --ALNGKELG 65

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

 Score = 73.7 bits (181), Expect = 2e-16
 Identities = 30/78 (38%), Positives = 50/78 (64%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
           +  K+FVGG++  TS   ++ +F+++GK+ E V+++D  TKR RGFGF+TF + +  D  
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 308 CEIHFHMIKNKKVECKKA 325
            E   H I   ++E K+A
Sbjct: 61  MEAQPHSIDGNQIELKRA 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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 72.3 bits (177), Expect = 3e-16
 Identities = 31/75 (41%), Positives = 50/75 (66%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVGG+S DTS +++K YF++FG+V +  + MD  T R RGFGF+ F++   V+ + E 
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 311 HFHMIKNKKVECKKA 325
             H +  + ++ 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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVG L+   + E LR+YF  FG VTDV I K       R F F+TFA+PE  + +   
Sbjct: 2   KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCG- 55

Query: 223 PIHTLDGKKI 232
             H + G  +
Sbjct: 56  EDHIIKGVSV 65

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

 Score = 72.7 bits (178), Expect = 3e-16
 Identities = 37/80 (46%), Positives = 51/80 (63%), Gaps = 1/80 (1%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           DP   K+FVGGL+ + + EK+REYFG FG +  + +  DP T + RGF FITF E + V+
Sbjct: 2   DPVK-KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60

Query: 218 KVLKVPIHTLDGKKIDPKHA 237
           KVL+   H + G K + K A
Sbjct: 61  KVLEKKFHNVSGSKCEIKVA 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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 72.8 bits (178), Expect = 4e-16
 Identities = 30/80 (37%), Positives = 51/80 (63%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           KK+FVGG+ +DT    ++ YF ++GK++   ++ D+Q+ + RGFGFVTF++ + VD I  
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 310 IHFHMIKNKKVECKKAQPKE 329
             +H I     E +KA  ++
Sbjct: 61  QKYHTINGHNAEVRKALSRQ 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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 72.3 bits (177), Expect = 4e-16
 Identities = 35/75 (46%), Positives = 47/75 (62%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S DT  E+++ YF  FG+VE   + MD +T + RGF F+TF+ EE V  I E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 311 HFHMIKNKKVECKKA 325
            +H +   K E K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

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

 Score = 71.9 bits (176), Expect = 6e-16
 Identities = 31/76 (40%), Positives = 49/76 (64%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           KKIFVGG++ + + E+++ YF +FG++E   + MD +T + RGF F+TF+ E+ V  + E
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

Query: 310 IHFHMIKNKKVECKKA 325
             FH +   K E K A
Sbjct: 65  KKFHNVSGSKCEIKVA 80

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

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

 Score = 71.2 bits (175), Expect = 8e-16
 Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 5/72 (6%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFVG L   T+ E LRE F  FG +  V I++D    +S+GF F+ F  PE  EK L+  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALE-- 57

Query: 224 IHTLDGKKIDPK 235
              L+GK++D +
Sbjct: 58  --ALNGKELDGR 67

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

 Score = 76.5 bits (187), Expect = 1e-15
 Identities = 46/239 (19%), Positives = 88/239 (36%), Gaps = 30/239 (12%)

Query: 92  PNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQ------LVLVNGKS 145
            +    L + + K   +    +      +  K         +   +            +S
Sbjct: 42  NSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRS 101

Query: 146 SGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
           S        + ++  +  LFVG L +  + E LRE F  FG V  V +++D  T +SRGF
Sbjct: 102 SESPKSRQKSKEENNT--LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGF 159

Query: 206 GFITFAEPETVEKVLKVPIHT-LDGKKIDPKHATPKNRPKI------------------- 245
            F+ F   E+ EK ++      L+G+ +  + A P ++P+                    
Sbjct: 160 AFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKA 219

Query: 246 --GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
               ++  ++VG +   T+ EE+   F   G +    +   +  K  +   FV  E  +
Sbjct: 220 LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASK 278

Length = 306

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

 Score = 70.9 bits (174), Expect = 1e-15
 Identities = 30/71 (42%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            LFVG LSW    E L+  F  FG V    ++ D  T RSRGFG++ F  PE  +K    
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA--- 57

Query: 223 PIHTLDGKKID 233
            I  +DGK++D
Sbjct: 58  -IEAMDGKELD 67

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

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 23/73 (31%), Positives = 47/73 (64%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVG +     ++E+K YFSQFGKV+   +  D++T   +G+GFV+F + + +++  + 
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 311 HFHMIKNKKVECK 323
             H+++  K++ +
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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 77.9 bits (192), Expect = 2e-15
 Identities = 61/239 (25%), Positives = 101/239 (42%), Gaps = 40/239 (16%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+V  L    + +KLRE F  FG +T   +MKD  + RSRGF F+ F + E   K     
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKA---- 235

Query: 224 IHTLDGKKIDP----------------------------KHATPKNRPKIGNRTKKIFVG 255
           +  ++GKKI                                   K + +  N    ++V 
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVN----LYVK 291

Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHM 314
            +    + E+++  FS+ G++    +++D++    RGFGFV F N EE    + E+H  M
Sbjct: 292 NLDDTVTDEKLRELFSECGEITSAKVMLDEK-GVSRGFGFVCFSNPEEANRAVTEMHGRM 350

Query: 315 IKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQV 373
           +  K +    AQ KE  +A+L   + + L P   ++   +P+  A        Q   Q 
Sbjct: 351 LGGKPLYVALAQRKEQRRAHLQD-QFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQ 408

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

 Score = 70.0 bits (171), Expect = 3e-15
 Identities = 32/75 (42%), Positives = 50/75 (66%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S  T+ E ++ YF QFG+V+E +++ D  TKR RGFGFVTF ++  VD +   
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 311 HFHMIKNKKVECKKA 325
             H + +K ++ 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 69.5 bits (171), Expect = 3e-15
 Identities = 22/71 (30%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
           +FVG +  DT+ E++K  FS+FG +E  + ++  +T R +GF FV FE+EE  +  +  +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIES-IRIVRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 311 HFHMIKNKKVE 321
           +   +  +++ 
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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 31/78 (39%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++FVGG+   T+ E+LR++F  FG+V DV I+ D     S+G+GF+TF   E  EK+L +
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGV-SKGYGFVTFETQEDAEKILAM 62

Query: 223 PIHTLDGKKIDPKHATPK 240
                 GKK++   A  K
Sbjct: 63  GNLNFRGKKLNIGPAIRK 80

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

 Score = 69.6 bits (170), Expect = 4e-15
 Identities = 30/76 (39%), Positives = 49/76 (64%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S DTS +++  Y S+FG+V +  +  D  T R RGFGFV F++   VD + E+
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 311 HFHMIKNKKVECKKAQ 326
             H +  K ++ K+A+
Sbjct: 61  KEHKLDGKLIDPKRAK 76

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|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 = 69.1 bits (169), Expect = 6e-15
 Identities = 25/52 (48%), Positives = 42/52 (80%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K+F+GG+S DT+ + ++  FS++G++ E V++ D++T+R RGFGFVTFEN +
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPD 53

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

 Score = 74.6 bits (182), Expect = 7e-15
 Identities = 29/92 (31%), Positives = 52/92 (56%), Gaps = 1/92 (1%)

Query: 238 TPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
           +PK+R K       +FVG +  D + E+++  F +FG V+   ++ D++T + RGF FV 
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVE 163

Query: 298 FENEEVVDHICEI-HFHMIKNKKVECKKAQPK 328
           FE+EE  +   E  +   ++ + +  +KAQP 
Sbjct: 164 FESEESAEKAIEELNGKELEGRPLRVQKAQPA 195

Length = 306

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

 Score = 68.5 bits (167), Expect = 9e-15
 Identities = 30/74 (40%), Positives = 49/74 (66%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +F+GG+S DT+ +++K YFS+FG+V +  + +D  T R RGFGFV F+  E VD + +  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 312 FHMIKNKKVECKKA 325
            H +  K ++ K+A
Sbjct: 61  EHKLNGKVIDPKRA 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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 68.4 bits (167), Expect = 1e-14
 Identities = 26/77 (33%), Positives = 51/77 (66%), Gaps = 1/77 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +F+GG++ +T+ + ++ YF QFG+V +  ++ D  T R RGFGF+TF+  + V+ + +  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 312 FHMIKNKKVECKKAQPK 328
            H++  K ++ K+A P+
Sbjct: 61  -HILDGKIIDPKRAIPR 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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 67.9 bits (166), Expect = 2e-14
 Identities = 29/78 (37%), Positives = 49/78 (62%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVGG+S +T+ E ++ YFSQ+G+V + V++ D+ T R RGFGFV F++   V  +   
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 311 HFHMIKNKKVECKKAQPK 328
             H +  + ++ K   P+
Sbjct: 61  GPHTLDGRTIDPKPCTPR 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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 67.6 bits (165), Expect = 2e-14
 Identities = 28/74 (37%), Positives = 49/74 (66%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +FVGG+S DT+ +++K YFS+FG+V +  + +D  T R RGFGFV F++   V+ + +  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 312 FHMIKNKKVECKKA 325
            H +  + ++ K+A
Sbjct: 61  EHKLDGRVIDPKRA 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 67.3 bits (164), Expect = 2e-14
 Identities = 28/78 (35%), Positives = 47/78 (60%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGG+   T    LR+YF  +G +  + +M+D  + + RGF F+TF + +TV+K++  
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 223 PIHTLDGKKIDPKHATPK 240
             HT++G   + K A  K
Sbjct: 62  KYHTINGHNCEVKKALSK 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 69.3 bits (169), Expect = 3e-14
 Identities = 33/76 (43%), Positives = 44/76 (57%), Gaps = 4/76 (5%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S KLF+GGLSW T    LR+ F  FG V D  ++ D  T RSRGFGF+ F +    E   
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFND----EGAA 89

Query: 221 KVPIHTLDGKKIDPKH 236
              I  +DGK+++ +H
Sbjct: 90  TAAISEMDGKELNGRH 105

Length = 144

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

 Score = 66.8 bits (164), Expect = 3e-14
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV- 222
           L+V  L    + E LRE+F  +G V  V ++++    R RGF F+ FA PE  E  LK  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 223 PIHTLDGKKI 232
               LDG+ +
Sbjct: 59  NGLVLDGRTL 68

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

>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 = 66.9 bits (164), Expect = 4e-14
 Identities = 27/52 (51%), Positives = 40/52 (76%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K+FV G+S  T+ +E++A FS+FG+VEE +++ D +T   RGFGFVTFE+ E
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVE 54

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

 Score = 66.7 bits (162), Expect = 5e-14
 Identities = 31/76 (40%), Positives = 48/76 (63%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+F+GG+S +T+ E ++ Y+ Q+GK+ + V++ D  +KR RGFGFVTF     VD    
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 310 IHFHMIKNKKVECKKA 325
              H I  + 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 21/73 (28%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I 310
           +FVG +  DT+ E+++  FS+FG++E   ++ D +  + +GF FV FE+ E  +   E +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 311 HFHMIKNKKVECK 323
           +   +  +K++  
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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 66.3 bits (161), Expect = 6e-14
 Identities = 31/75 (41%), Positives = 49/75 (65%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S  TS + ++ YFS+FG++ E +++ D  TKR RGFGFVTF +   VD +   
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 311 HFHMIKNKKVECKKA 325
             H + +K ++ K A
Sbjct: 61  PHHELDSKTIDPKVA 75

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

 Score = 66.2 bits (161), Expect = 6e-14
 Identities = 30/75 (40%), Positives = 47/75 (62%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T+ E+++EYFG FG + ++ +  D  T   RGF F+T+ + E V+K+L+ 
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 223 PIHTLDGKKIDPKHA 237
             H +   K + K A
Sbjct: 61  RYHQIGSGKCEIKVA 75

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

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

 Score = 66.1 bits (162), Expect = 6e-14
 Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           +IFVGG+  DT+ EE++ +FS+FG V++  ++ D +    +G+GFVTFE +E  + I  +
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 311 HFHMIKNKKVECKKA 325
                + KK+    A
Sbjct: 63  GNLNFRGKKLNIGPA 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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 66.2 bits (161), Expect = 7e-14
 Identities = 30/76 (39%), Positives = 50/76 (65%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+ + E VD    
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 310 IHFHMIKNKKVECKKA 325
              H +  + VE K+A
Sbjct: 63  ARPHKVDGRVVEPKRA 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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 65.8 bits (161), Expect = 7e-14
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+FVG +++D + E+++ YFSQFG+V +  +      K  R F FVTF + EV   +C 
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI-----PKPFRAFAFVTFADPEVAQSLCG 55

Query: 310 IHFHMIKNKKV 320
              H+IK   V
Sbjct: 56  -EDHIIKGVSV 65

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

 Score = 66.1 bits (162), Expect = 7e-14
 Identities = 21/49 (42%), Positives = 34/49 (69%)

Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           V G+S  T+  +++  FS++G +E+  ++ DQ+T R RGFGFV FE+ E
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVE 52

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

 Score = 65.8 bits (161), Expect = 8e-14
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L+++T+ + LR  F  +G V DV I +D  T+ SRGF F+ F +    E      
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA---- 56

Query: 224 IHTLDGKKIDPKH 236
           +  +DGK++D + 
Sbjct: 57  MDAMDGKELDGRE 69

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

 Score = 65.8 bits (160), Expect = 9e-14
 Identities = 35/75 (46%), Positives = 46/75 (61%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T  EK+REYFG FG V  + +  D  T + RGF FITF E E V+K+++ 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 223 PIHTLDGKKIDPKHA 237
             H +   K + K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

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

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 20/55 (36%), Positives = 33/55 (60%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
            ++VG +  + + E++K  F QFG+V    ++ D++T R RGFGFV  E  E  +
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEAN 55

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

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFV  L++ T+  KLR  F  +G +  + +++D  T + RG+ FI F      E+ +K  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEH----ERDMKAA 59

Query: 224 IHTLDGKKID 233
               DGKKID
Sbjct: 60  YKYADGKKID 69

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

 Score = 70.7 bits (173), Expect = 3e-13
 Identities = 48/173 (27%), Positives = 80/173 (46%), Gaps = 26/173 (15%)

Query: 149 SGRSTP---TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
           SGR+T    T  +     +FV  L+ +     L E+F   G V DV  +KD  ++RS+G 
Sbjct: 74  SGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGV 133

Query: 206 GFITFAEPETV--------EKVLKVPIHTLDGKKIDPKHATPKNR--------PKIGNRT 249
            ++ F + E+V        + +L  PI       +    A  KNR        P      
Sbjct: 134 AYVEFYDVESVIKALALTGQMLLGRPI------IVQSSQAE-KNRAAKAATHQPGDIPNF 186

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            K++VG +  + + +E++  F  FG +E+  +  D +T R +GFGF+ F + E
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE 239

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

 Score = 63.9 bits (155), Expect = 5e-13
 Identities = 26/75 (34%), Positives = 45/75 (60%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGG+   T    LR+YF  +G +  + IM D  + + RGF F+TF + ++V+K++  
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

Query: 223 PIHTLDGKKIDPKHA 237
             HT++G   + + A
Sbjct: 62  KYHTVNGHNCEVRKA 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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 63.1 bits (154), Expect = 7e-13
 Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFVG LSW    + L E+F   G V DV I +D    RS+GFG + FA  E  +K L+  
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEKS 60

Query: 224 IHTLDGKKIDPKHATPK 240
              L G++I    AT +
Sbjct: 61  GEELLGREIRVDLATER 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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 62.8 bits (152), Expect = 1e-12
 Identities = 29/76 (38%), Positives = 49/76 (64%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+F+GG+S +T+ + ++ +F ++G + + V++ D QTKR RGFGFVT+   E VD    
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 310 IHFHMIKNKKVECKKA 325
              H +  + VE K+A
Sbjct: 63  ARPHKVDGRVVEPKRA 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 62.6 bits (152), Expect = 1e-12
 Identities = 29/78 (37%), Positives = 42/78 (53%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVGGL        L E+F  FG V    ++ D  T + RGFGF+ F   ++ +K   V
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 223 PIHTLDGKKIDPKHATPK 240
             H ++G +++ K A PK
Sbjct: 61  KFHPINGHRVEVKKAVPK 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           ++V  +    + E+++ +FS +GKVE   ++ ++   R RGF FV F + E  +   +  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 312 -FHMIKNKKVE 321
              ++  + + 
Sbjct: 59  NGLVLDGRTLR 69

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

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

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           L+VG L +  + + LR  F  FG +  V + +DP T RS+G+GFI FA+ E  +K L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57

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

 Score = 67.4 bits (164), Expect = 4e-12
 Identities = 54/238 (22%), Positives = 97/238 (40%), Gaps = 43/238 (18%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-K 221
           +++VG +S++   + +R  F  FG +  + +  DP T + +GF F+ +  PE  +  L +
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 222 VPIHTLDGKKIDPKHATPKNRP----------KIGNRTKKIFVGGVSQDTSAEEVKAYFS 271
           +    L G+ I  K   P N P          +   +  +I+V  V  D S  ++K+ F 
Sbjct: 169 MNGQMLGGRNI--KVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFE 226

Query: 272 QFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAV 331
            FG++ +  +      + H+G+GF+ + N                       ++Q +   
Sbjct: 227 AFGEIVKCQLARAPTGRGHKGYGFIEYNN----------------------LQSQSEAIA 264

Query: 332 QANLL--------VGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVA 381
             NL         VGK V      L+ A  + I  A  +AA  + A+     A A  A
Sbjct: 265 SMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAA 322

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

 Score = 60.3 bits (147), Expect = 6e-12
 Identities = 18/51 (35%), Positives = 34/51 (66%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++VGG++++   + + A F  FG +++  + +D +T++HRGF FV FE  E
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51

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

 Score = 65.7 bits (160), Expect = 7e-12
 Identities = 39/151 (25%), Positives = 74/151 (49%), Gaps = 12/151 (7%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +   L V  L    + E++R  F   G +    +++D +T +S G+GF+ +  PE  EK 
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 220 LKVPIHTLDG-----KKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG 274
               +++L+G     K I   +A P +    G     ++V G+ +  +  E+++ FS FG
Sbjct: 62  ----VNSLNGLRLQNKTIKVSYARPSSDSIKG---ANLYVSGLPKTMTQHELESIFSPFG 114

Query: 275 KVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++  + +L D  T   +G GF+ F+  +  D
Sbjct: 115 QIITSRILSDNVTGLSKGVGFIRFDKRDEAD 145

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

 Score = 60.5 bits (146), Expect = 8e-12
 Identities = 27/78 (34%), Positives = 46/78 (58%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVGG+   T    LR+YF  +G +  + I+ D  + + RGFGF+TF + + V+K++  
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 223 PIHTLDGKKIDPKHATPK 240
             HT++G   + + A  +
Sbjct: 62  KYHTINGHNAEVRKALSR 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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 60.1 bits (146), Expect = 9e-12
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            + V G+   T+ +++K YFS FG++    +  D +T + +GFGFV F + E    +   
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 311 HFHMIKNKKVECKKAQPK 328
             HMI  +  + K    K
Sbjct: 61  R-HMIDGRWCDVKIPNSK 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 60.3 bits (147), Expect = 9e-12
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           +F+  L +  + E+L+E F  FG V    I+KD +T  S+G  F+ F   E+ +K L+
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

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

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++V  L      EKL+E FG +G +T   +MKD    +S+GFGF+ F   E  +K ++  
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE-- 60

Query: 224 IHTLDGKKIDPK 235
              L+GK+++ K
Sbjct: 61  --ELNGKEVNGK 70

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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 7/73 (9%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG-FGFITFAEPETVEKVLKV 222
           +FV G    TS E+L +YF  FG V +V++ KD      +G +  + F   E V+KVL  
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKVLSE 58

Query: 223 PIHTLDGKKIDPK 235
           P HTL+G ++  +
Sbjct: 59  PQHTLNGHRLRVR 71

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

 Score = 58.3 bits (142), Expect = 3e-11
 Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 169 LSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD 228
           LS     + LRE F  FG ++ V + KD  T +SRGF F+TF   E  E+ ++     L+
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE----KLN 62

Query: 229 GKKID 233
           G   D
Sbjct: 63  GFGYD 67

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

 Score = 57.2 bits (139), Expect = 7e-11
 Identities = 22/51 (43%), Positives = 30/51 (58%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
           L+VGGL+ +   + L   F  FG + D+ I  D  TQ+ RGF F+ F EPE
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51

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|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 18/52 (34%), Positives = 33/52 (63%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K+FVG + +  + E+V+A F ++G +EE  ++ D+ T + +G  FV F + E
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSRE 52

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

 Score = 57.0 bits (138), Expect = 9e-11
 Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 4/69 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FVG LS +  +E LR  F  FG ++D  ++KD  T +S+G+GF++F + E  E      
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA---- 57

Query: 224 IHTLDGKKI 232
           I +++G+ +
Sbjct: 58  IQSMNGQWL 66

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

 Score = 62.9 bits (153), Expect = 1e-10
 Identities = 48/149 (32%), Positives = 71/149 (47%), Gaps = 17/149 (11%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL- 220
           A L+VG L    +  KL + F  FG V  V + +D +T+RS G+G++ F  P   E+ L 
Sbjct: 1   ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE 60

Query: 221 KVPIHTLDGKKI-------DPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQF 273
            +    L GK I       DP       R  +GN    IFV  + +    + +   FS+F
Sbjct: 61  TMNFKRLGGKPIRIMWSQRDPS----LRRSGVGN----IFVKNLDKSVDNKALFDTFSKF 112

Query: 274 GKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           G +    +  D +  + RG+GFV FE EE
Sbjct: 113 GNILSCKVATD-ENGKSRGYGFVHFEKEE 140

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|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 = 56.8 bits (138), Expect = 1e-10
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVG L    + E +R  F  +G + +V I++D  T +S+G  F+ F+  E  +K    
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA--- 57

Query: 223 PIHTLDGKKIDP 234
            I  L GK   P
Sbjct: 58  -IEALHGKVTMP 68

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

 Score = 62.2 bits (151), Expect = 2e-10
 Identities = 29/67 (43%), Positives = 43/67 (64%)

Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           GD P   KL+VG L +  + ++LR+ F  FG + DV + +DP T RS+GFGFI F + E 
Sbjct: 181 GDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE 240

Query: 216 VEKVLKV 222
            ++ L+V
Sbjct: 241 AKEALEV 247

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|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 = 56.5 bits (137), Expect = 2e-10
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 4/68 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           +LFV  L + T+ E+LRE F  FG +++V +  D  T+RS+GF F++F  PE   K    
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYS- 59

Query: 223 PIHTLDGK 230
               LDG 
Sbjct: 60  ---ELDGS 64

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
           LFV  L + T+ E+L E+F   G +    ++KD  +++ RGFG++TFA  E  ++ L+  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 223 PIHTLDGKKIDPKHATPK 240
                 G+KI  + 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 19/51 (37%), Positives = 35/51 (68%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +FV  +  DT+ E+++ +FS+ G ++   ++ D+ +K+ RGFG+VTF  EE
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEE 52

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 15/53 (28%), Positives = 34/53 (64%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K +FV  ++ DT+  +++  F ++G ++   ++ D++T + RG+ F+ FE+E 
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 18/52 (34%), Positives = 34/52 (65%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +I+V  V  D S +++K+ F  FGK++   +  D +T +H+G+GF+ +EN +
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQ 53

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

 Score = 61.0 bits (148), Expect = 4e-10
 Identities = 43/180 (23%), Positives = 83/180 (46%), Gaps = 10/180 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK-VLKV 222
           +FV  L     ++ L + F  FG +    +  D    +SRG+GF+ F + E+ +  + KV
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 223 PIHTLDGKKIDPKHATPKNRPKIGNRTK--KIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
               L+ K++       K+  +     K   ++V  +    + ++++  F++FG++    
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA 209

Query: 281 MLMDQQTKRHRGFGFVTFENEE----VVDHICEIHFHMIKN-KKVECKKAQPKEAVQANL 335
           ++ D  + R RGF FV FE  E     V+ +      + K  KK+   +AQ +   +A L
Sbjct: 210 VMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAEL 268

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|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 = 55.4 bits (134), Expect = 4e-10
 Identities = 19/52 (36%), Positives = 33/52 (63%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++FV  +   T+ EE++  F  FG++ E  + +D++TKR +GF FV+F   E
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPE 52

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

 Score = 55.2 bits (134), Expect = 4e-10
 Identities = 25/68 (36%), Positives = 38/68 (55%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
           FVG L +    E+LR++F   G V  V I++D  T   +GFG++ F   ++V   LK+  
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

Query: 225 HTLDGKKI 232
             L G+KI
Sbjct: 63  IKLKGRKI 70

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

 Score = 55.2 bits (133), Expect = 5e-10
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE-TVEKVLKV 222
           LFV  L++  + E L ++F     +   +++ DP T  SRG+GF+TFA  E   E + K+
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 223 PIHTLDGKKIDPKHATPK 240
               L G+ +    A  +
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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 22/59 (37%), Positives = 39/59 (66%), Gaps = 1/59 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           ++FVGG+ ++T+   LR++F  +G V +V I+ D     S+G+GF+TF   E  +K+L+
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQ 61

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

 Score = 55.1 bits (133), Expect = 6e-10
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           P S +LFVG L    + ++L+E+F  FG V +V I       R   FGF+ F +PE V+K
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 219 VL-KVPIHTLDGKKID 233
           +L   PI+     +++
Sbjct: 61  ILANKPIYFRGDHRLN 76

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

 Score = 54.7 bits (132), Expect = 8e-10
 Identities = 26/69 (37%), Positives = 38/69 (55%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFVG L + T++E L  +F   GA   V ++ D  T +S+G  F+ F   E + K LK+ 
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 224 IHTLDGKKI 232
              L G+KI
Sbjct: 63  HTLLKGRKI 71

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

 Score = 54.6 bits (132), Expect = 8e-10
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 5/71 (7%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           +L V  L ++ +   L++ F  FG V +V I + P   + +GF F+ F      EK +K 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIK- 58

Query: 223 PIHTLDGKKID 233
               ++GKKI 
Sbjct: 59  ---GVNGKKIK 66

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 25/54 (46%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           L V GLS  T+   LRE F  +G +  V ++ D  T RSRGFGF+ F   E+VE
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYF---ESVE 52

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           + +F+  +  D + EE+K  FSQFG+V+   ++ D+ T   +G  FV F+ +E      E
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

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

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 17/51 (33%), Positives = 30/51 (58%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +FVG +  D + E++   FS+ G V    ++ D+ T + +G+GF  FE+ E
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIE 51

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 14/83 (16%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
           ++G L+W  + + +RE+F     +T V +  D  T   +GFG + FA+ E+++  LK   
Sbjct: 3   YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK--- 58

Query: 225 HTLDGKKIDPKHATPKNRP-KIG 246
             LDG  +         RP +I 
Sbjct: 59  --LDGTVL-------CGRPIRIA 72

The CD corresponds to the RRM2 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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVT--DVLIMKDPITQRSRGFGFITFAEPETVEK 218
           +  L + GL   T+ E + +      +V   DV +++D +T  SRGF F+ F   E   +
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 219 VLK----VPIHTLDGKKI 232
            +     +    +DG+ +
Sbjct: 62  WMDALNNLDPFVIDGRVV 79

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 22/52 (42%), Positives = 32/52 (61%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            +FVG +S     E +KA F +FG V    ++ D++T R RGFG+V FE+ E
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPE 52

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
             L+V  L      E+LRE F  FG +T   +M D    RS+GFGF+ F+ PE   K   
Sbjct: 2   VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATK--- 57

Query: 222 VPIHTLDGKKIDPK 235
             +  ++G+ I  K
Sbjct: 58  -AVTEMNGRIIGGK 70

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

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 4/67 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FVG LS + +   L   F  F + +D  +M D  + RSRG+GF++F   +  E      
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA---- 57

Query: 224 IHTLDGK 230
           I+ ++GK
Sbjct: 58  INEMNGK 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 54.3 bits (130), Expect = 4e-09
 Identities = 21/53 (39%), Positives = 35/53 (66%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           + K+F+GG+S  T    ++  F+ FG V +  +++D++T R RGFGFV F +E
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDE 86

Length = 144

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           + +LFV  L +    + L + F  FG +++V +  D  + +S+GF ++ F +PE   K  
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61

Query: 221 KVPIHTLDGKK 231
           K     LDGK 
Sbjct: 62  K----ELDGKV 68

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

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

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 8/81 (9%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVDHI 307
           ++V  + +D   E++K  F ++GK+    ++ D + K  +GFGFV FEN E     V+  
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS-KGFGFVNFENHEAAQKAVE-- 60

Query: 308 CEIHFHMIKNKKVECKKAQPK 328
            E++   +  KK+   +AQ K
Sbjct: 61  -ELNGKEVNGKKLYVGRAQKK 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 52.5 bits (126), Expect = 5e-09
 Identities = 16/51 (31%), Positives = 29/51 (56%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +FV  ++   + E++  +FS    ++  V++ D +T   RG+GFVTF   E
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLE 52

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

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 11/86 (12%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
                ++FVG L  + + E L   F  + +     +++D  T +S+G+GF++F++P    
Sbjct: 3   PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62

Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRP 243
           K +K     ++GK +        NRP
Sbjct: 63  KAMK----EMNGKYVG-------NRP 77

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 17/69 (24%), Positives = 38/69 (55%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           IFVG V   T+ EE++ +F   G +    +L D+ T + +GF ++ F ++  V++   ++
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61

Query: 312 FHMIKNKKV 320
               + +++
Sbjct: 62  ESEFRGRQI 70

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

 Score = 52.0 bits (125), Expect = 8e-09
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+V  ++  T  + LR  FG +G + DV I  D  T+R RGF ++ F +    E  L   
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL--- 59

Query: 224 IHTLDGKKI 232
            + LD  + 
Sbjct: 60  -YYLDRTRF 67

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|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 = 51.5 bits (124), Expect = 9e-09
 Identities = 17/53 (32%), Positives = 27/53 (50%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           FVG + +  + E+L E F   G V    ++ D  T + +G+GF  F + ET  
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAA 54

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

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           IFVG +S D + EE+   FS+ GK+ E  ++  ++      F F+ FE E+      E  
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 312 FH-MIKNK--KVECK 323
            H M+KNK   V+ K
Sbjct: 64  NHSMLKNKTMHVQYK 78

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++VGG+ + ++ +++R YF   G + ++ +M  P T R RG  FITF   E  ++ L   
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-- 58

Query: 224 IHTLDGKKID 233
              LDG+ + 
Sbjct: 59  ---LDGEDMG 65

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR------GFGFITFAEPETV 216
           +++V  L ++   + LR  F  FG V  + I   P  Q  +      GF F+TF +  + 
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRI---PKKQDEKQGRLNNGFAFVTFKDASSA 58

Query: 217 EKVLKVPIHTLDGKKID 233
           E  L++    L G+KI 
Sbjct: 59  ENALQLNGTELGGRKIS 75

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

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVEC 322
            E++ YFSQFG V    +   ++T + +G+ FV FE+ EV   + E ++ +++  + ++C
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73

Query: 323 K 323
           K
Sbjct: 74  K 74

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

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 19/51 (37%), Positives = 34/51 (66%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           IFVG +S +   E ++A F+ FG++ +  ++ D QT + +G+GFV+F  +E
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKE 52

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 21/69 (30%), Positives = 40/69 (57%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +FVG +  DT+AE++ A+F   G      +L D++T + +G  FV F+  E +    ++H
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 312 FHMIKNKKV 320
             ++K +K+
Sbjct: 63  HTLLKGRKI 71

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFVG LS+    + + E FG +G ++ V +  DP + R +GFG++ F+  E  +  L   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 224 IHT-LDGKKI 232
             T L G+ +
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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 16/53 (30%), Positives = 31/53 (58%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV 304
           +FV  +S      ++  +FS+ GKV +  ++ D+ ++R +G  +V F +EE 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFVG LS++T+ ++LR +FG  G +  V +M    + + +GF F+ F E E     LK  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 224 I 224
            
Sbjct: 61  H 61

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           ++ V  L    + ++LRE+F   G VTDV +M+     +SR FGF+ F   E  ++ +K
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59

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

 Score = 50.1 bits (120), Expect = 3e-08
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S +LF+  L++  + E L + F  +G +++V +  D +T++ +GF F+T+  PE   K  
Sbjct: 2   SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61

Query: 221 KVPIHTLDG 229
                 LDG
Sbjct: 62  A----ELDG 66

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

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

 Score = 50.2 bits (120), Expect = 4e-08
 Identities = 23/69 (33%), Positives = 43/69 (62%), Gaps = 2/69 (2%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FVGG+  +    ++R +F  +G+V +V I+ D  T  S+G+GF++F +   V+K+++  
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 224 IHTLDGKKI 232
           I    GKK+
Sbjct: 67  I-NFHGKKL 74

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

 Score = 50.0 bits (119), Expect = 4e-08
 Identities = 31/83 (37%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           R+ P   DP    L V GLS  T+   LRE F  +G + DV I+ D  ++RSRGF F+ F
Sbjct: 3   RANP---DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58

Query: 211 AEPE-TVEKVLKVPIHTLDGKKI 232
              +   E   +     LDG++I
Sbjct: 59  ENVDDAKEAKERANGMELDGRRI 81

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 49.9 bits (119), Expect = 4e-08
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FVG L ++   E L   FG  G +  V I++DP T   +GF ++ F +   VEK L   
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL--- 58

Query: 224 IHTLDGKKIDPKHA 237
              L+ KK  P   
Sbjct: 59  --LLNEKKFPPMLP 70

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 49.5 bits (118), Expect = 5e-08
 Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVG L+ Q + +++ E F  +G V D+ +M+D + Q SRG  F+ ++  E  +  +K 
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQ-SRGCAFVKYSSKEMAQAAIKA 59

Query: 223 --PIHTLDG 229
              ++T+ G
Sbjct: 60  LNGVYTMRG 68

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

 Score = 49.3 bits (118), Expect = 6e-08
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 7/79 (8%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR-SRGFGFITFAEPETVEKVLK 221
           +L V  + ++     LR+ FG FG + DV I+     +R S+GFGF+TFA     ++  +
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEII---FNERGSKGFGFVTFANSADADRA-R 57

Query: 222 VPIH--TLDGKKIDPKHAT 238
             +H   ++G+KI+  +AT
Sbjct: 58  EKLHGTVVEGRKIEVNNAT 76

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

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

 Score = 49.3 bits (117), Expect = 8e-08
 Identities = 19/49 (38%), Positives = 33/49 (67%)

Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV FEN +
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62

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

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLI-----MKDPITQRSRGFGFITFAEPETVEK 218
           LFV  L+++T+ E L+++F   G V  V I      K P    S G+GF+ F   E  +K
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 219 VLKVPIHT-LDGKKID 233
            LK    T LDG  ++
Sbjct: 63  ALKRLQGTVLDGHALE 78

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

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

 Score = 48.8 bits (117), Expect = 8e-08
 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDPITQRSRGFGFITFA 211
           A LF+G L  +   + L + F  FG  +    IM+DP T  S+GF FI++ 
Sbjct: 2   ANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYD 52

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

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 22/57 (38%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
           +IFVGG+   T+  +++ +FSQ+G V+E V +++ +    +G+GFVTFE +E    I
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKE-VKIVNDRAGVSKGYGFVTFETQEDAQKI 59

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

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           IFVG +S + +   + A FS F    +  ++ D ++ R RG+GFV+F +++
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQ 52

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           FV  LS +     L E+F   G V DV I++D  ++RS+G  ++ F + E+V   L
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58

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

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           + LFV  ++  T SE LR  FG +G + DV +  D  T+R RGF ++ F +    E  L 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL- 59

Query: 222 VPIHTLDGKKI 232
              H LD K I
Sbjct: 60  ---HNLDRKWI 67

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 19/49 (38%), Positives = 31/49 (63%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
           LFVG LS QT+ E LRE F  +G +  + +++D +T  S+G+ F+ +  
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEH 54

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

 Score = 48.3 bits (116), Expect = 1e-07
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L VG L+   + + L+E F  +G V DV +  D      RG+ ++ F  PE  EK +K  
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK-- 58

Query: 224 IHTLDGKKID 233
            H +DG +ID
Sbjct: 59  -H-MDGGQID 66

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 14/51 (27%), Positives = 31/51 (60%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++VG +  + + ++++  F  FG++E   +  D +T R +G+GF+ F + E
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAE 51

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 21/68 (30%), Positives = 38/68 (55%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
           FVG + + T+ E+L+E+F   G +  + I+ D  T + +GF +I F +  +VE  L +  
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

Query: 225 HTLDGKKI 232
               G++I
Sbjct: 63  SEFRGRQI 70

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FV  L        L + F  FGAVT+V +++D  T + +G+GF+T    E  E      
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAY--SA 59

Query: 224 IHTLDGKKIDPK 235
           I +L+G ++  +
Sbjct: 60  IASLNGYRLGGR 71

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           ++VG + +  + E +   F Q G V    +  D+ T+ H+G+GFV F +EE  D+  +I 
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI- 59

Query: 312 FHMIK--NKKVECKK 324
            +MIK   K +   K
Sbjct: 60  MNMIKLYGKPIRVNK 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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           ++FVG +  D + +E+K +F +FG V E  +       R   FGFV F++ E V  I   
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 311 HFHMIKNKK---VECKK 324
                +      VE KK
Sbjct: 65  KPIYFRGDHRLNVEEKK 81

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 14/50 (28%), Positives = 33/50 (66%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           + ++F+  ++   + E+++  FS++G + E  + +D+ TK+ +GF FVT+
Sbjct: 2   SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51

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

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 17/52 (32%), Positives = 30/52 (57%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +++VG +S +   + ++  FS FG ++   M  D  T +H+GF FV +E  E
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPE 53

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|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 = 3e-07
 Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
           +F+  +  + + +++   F+ FG V    + +D+ T + + FGFV+++N E     I  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 311 HFHMIKNK--KVE 321
           +   +  K  KV+
Sbjct: 61  NGFQVGGKRLKVQ 73

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

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

 Score = 47.1 bits (113), Expect = 3e-07
 Identities = 19/58 (32%), Positives = 29/58 (50%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           L+VG L    +   L E F   G V  + + +D IT+RS G+ ++ F  P   E+ L 
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALD 59

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

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 15/46 (32%), Positives = 26/46 (56%)

Query: 257 VSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +S+D   ++++  F  FG +    +  D++T + RGF FVTF   E
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTRE 52

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

 Score = 47.0 bits (112), Expect = 4e-07
 Identities = 13/50 (26%), Positives = 31/50 (62%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           T ++FV  +      ++++  FS+FG++ E  + +D+++ + +GF +V F
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 51

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

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 18/50 (36%), Positives = 35/50 (70%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           +FVG +S + + E++K+ F+ FGK+ +  ++ D  T + +G+GFV+F N+
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 53

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

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK-VLKV 222
           +FVG LS + ++E ++  F  FG ++D  ++KD  T +S+G+GF++F      E  ++ +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 223 PIHTLDGKKIDPKHAT 238
               L G++I    AT
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

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

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I 310
           I++G +      +E+K YFSQFG V+   +   ++T   + +GF+ F N EV     + +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 311 HFHMIKNKKVECK 323
           + +++  K ++  
Sbjct: 62  NNYLLMGKVLQVH 74

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

 Score = 51.3 bits (123), Expect = 5e-07
 Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
             L+V  L    + EKLRE F   G +T   +M D     SRGFGF+ F+ PE   + + 
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 344

Query: 222 VPIHTLDGKKIDPK 235
                + G+ +  K
Sbjct: 345 ----EMHGRMLGGK 354

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

 Score = 46.8 bits (111), Expect = 5e-07
 Identities = 19/52 (36%), Positives = 35/52 (67%), Gaps = 1/52 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K+FVG +++  + +EV+  FS +G+VE+  M+ D+  K+ RG  FV + ++E
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKE 51

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|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 = 46.5 bits (111), Expect = 5e-07
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE- 309
           KIF+GG+    S ++VK     FGK++   ++ D  T   +G+ F  + +  V D     
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 310 IHFHMIKNKKVECKKA 325
           ++   + +KK+  ++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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 47.6 bits (113), Expect = 5e-07
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
           LFV  L +  + E L  +F  FG+V   L + D  T R++G GF+ F +  T    LK  
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 223 PIH 225
           P  
Sbjct: 64  PAA 66

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +FV  L +    ++LR+ F   G +TDV ++K+    +S+G+ ++ F   E+V++ LK+ 
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEALKLD 60

Query: 224 IHTLDGK 230
              + G+
Sbjct: 61  RELIKGR 67

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

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
           + E+LR  F   G +    I++D IT +S G+GF+ + +    +K     I+TL+G +I 
Sbjct: 13  TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA----INTLNGFEIR 68

Query: 234 PKH 236
            K 
Sbjct: 69  NKR 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 46.3 bits (110), Expect = 6e-07
 Identities = 17/51 (33%), Positives = 33/51 (64%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +FVG +S +T+ +E++A+F + G++    M+  + + + +GF FV FE  E
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51

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|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 = 46.1 bits (110), Expect = 6e-07
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LF+  L  + + + L + F  FG V    +  D  T +S+ FGF+++  PE+ +      
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA---- 56

Query: 224 IHTLDGKKIDPKH 236
           I  ++G ++  K 
Sbjct: 57  IKAMNGFQVGGKR 69

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

 Score = 47.2 bits (112), Expect = 6e-07
 Identities = 17/54 (31%), Positives = 32/54 (59%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           +FV  +  D + E +  +FS+FG V   + ++D+ T R +G GFV F+++   +
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN 57

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

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

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 19/52 (36%), Positives = 34/52 (65%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
           ++VGG+   ++ +E+++YFS  G++EE  ++    T R RG  F+TF+ EE 
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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVL- 220
           L+VG L+W T+ E L       G   V  +   +     +S+GF ++ FA       V  
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 221 KVPIHTLDGKK 231
           K+     +GKK
Sbjct: 61  KLEGREFNGKK 71

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

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

 Score = 46.0 bits (110), Expect = 7e-07
 Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF-AEPETVEKVLKV 222
           LFVGGLS   +   L E F  FG V+DV I+K       RGF +I        ++K    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

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

 Score = 46.1 bits (109), Expect = 8e-07
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 166 VGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE-TVEKVLKVPI 224
           V GLS  T+   LRE F  +G +  V ++ D  T RSRGF F+ F   + + E +     
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 225 HTLDGKKIDPKHATPK 240
             LDG++I   ++  K
Sbjct: 64  MELDGRRIRVDYSITK 79

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

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           LFVG L  + + E L E F   G +  V I KDP  +  + F F+TF    +V
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEVSV 55

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)

Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDG 229
            +LR+YF  FG VT + + +   T +S+G+ F+ F  PE    V K+   T++ 
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE----VAKIVAETMNN 63

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

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 3/69 (4%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-- 309
           +FVGG+       E++++F+++G V+E  ++ D +T   +G+GFV+F ++  V  I E  
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 310 IHFHMIKNK 318
           I+FH  K K
Sbjct: 67  INFHGKKLK 75

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++VG L  + + E L E F   G V +V I KD +TQ  +G+GF+ F   E  +  +K+
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59

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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 164 LFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           L++G L  W   +  +   F   G VT V I+++  T +S G+GF+ FA  E  E+ L  
Sbjct: 2   LWMGDLEPWMDEAY-IYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQAL-- 58

Query: 223 PIHTLDGKKI 232
              +L+GK I
Sbjct: 59  --QSLNGKPI 66

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

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +K+FVG +S+  +  +V+  F+ FG +EE  +L DQ  +  RG  FVTF + +
Sbjct: 2   RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQS-RGCAFVTFASRQ 53

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 49.6 bits (118), Expect = 1e-06
 Identities = 36/162 (22%), Positives = 68/162 (41%), Gaps = 4/162 (2%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
           N  +S  SG S     + +   L V  L    +  +L   F   G +    IM+D  T  
Sbjct: 88  NSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGY 147

Query: 202 SRGFGFITFAEPETVEKVLKVPIH-TLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQD 260
           S G+ F+ F      ++ +K     T+  K++   +A P        +   ++V  + + 
Sbjct: 148 SFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESI---KDTNLYVTNLPRT 204

Query: 261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            + +++   F ++G++ +  +L D+ T   RG  FV F   E
Sbjct: 205 ITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKRE 246

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 10/75 (13%)

Query: 251 KIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
           ++FVG ++ D  S E+++  FS++GK+    +        H+G+GFV F+NEE     + 
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 309 EIHFHMIKNKKVECK 323
             +   I  +K++  
Sbjct: 54  GENGREIAGQKLDIN 68

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

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR---GFGFVTFENEEVVDHI 307
           +I+V  +      ++++  FS+FG+VE   +   Q  K+ R   GF FVTF++    ++ 
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 308 CEIHFHMIKNKKVE 321
            +++   +  +K+ 
Sbjct: 62  LQLNGTELGGRKIS 75

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

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           + +   L V  L    + E+L+  FG  G +    +++D IT +S G+GF+ + +P+  E
Sbjct: 1   EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 218 KVLKVPIHTLDGKKIDPK 235
           K     I+TL+G ++  K
Sbjct: 61  KA----INTLNGLRLQTK 74

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|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 = 45.5 bits (108), Expect = 2e-06
 Identities = 17/48 (35%), Positives = 31/48 (64%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           K+FVG + ++   ++++  F QFGK+ E  +L D+ T  H+G  F+T+
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54

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

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +   L V  L    + E+ R  FG  G +    +++D IT +S G+GF+ + +P+  EK 
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 220 LKVPIHTLDGKKIDPK 235
               I+TL+G ++  K
Sbjct: 61  ----INTLNGLRLQTK 72

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 18/55 (32%), Positives = 26/55 (47%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           LFV  L+  T+ E L   F  FG +    +++D  T  S  + FI F   E  E+
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

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

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

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 9/68 (13%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           K+FVG +  + + +E+++ F Q+GKV E  ++        + +GFV  +++   D  I  
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 310 IHFHMIKN 317
           +H + +  
Sbjct: 54  LHHYKLHG 61

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           ++V G+S  T A ++K  FS++GKV    ++ + ++   R FGFVT  + E     C  H
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAK-CIQH 60

Query: 312 FH 313
            H
Sbjct: 61  LH 62

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 17/50 (34%), Positives = 35/50 (70%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           +FVG +S + + +++KA F+ FG++ +  ++ D  T + +G+GFV+F N+
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 53

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +FVG +S     ++++ +F + G+V + V +      R +GFG V F  EE      E  
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVD-VRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 312 FHMIKNKKVECKKAQPK 328
              +  +++    A  +
Sbjct: 61  GEELLGREIRVDLATER 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L VG L  + + E+ RE    FGAV    ++    T  S+G+GF+ +A   +  K  K  
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA-K-- 58

Query: 224 IHTLDGKKIDPKHA 237
            + LDGK+I  +  
Sbjct: 59  -NQLDGKQIGGRKL 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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 20/47 (42%), Positives = 30/47 (63%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           +FV  LS +     L + FG FGAVT+V +++D  T + +GFGF+T 
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTM 50

This subgroup corresponds to the RRM3 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 = 85

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 17/51 (33%), Positives = 30/51 (58%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++VG +S  T+ E++   FS+ G ++  +M +D+ TK   GF FV +   E
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTRE 51

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

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

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHIC 308
             ++V  V+  T  ++++  F ++G + +  + +D  T+R RGF +V FE+  +  D + 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 309 EIHFHMIKNKKVECKKAQ 326
            +       +++E + AQ
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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKV 219
           +FV  L ++   +KL+E F + G V    I +D    +SRG G + F  P E V+ +
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAI 56

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

 Score = 48.0 bits (114), Expect = 5e-06
 Identities = 32/147 (21%), Positives = 47/147 (31%), Gaps = 19/147 (12%)

Query: 82  PPQPQPRDLQPN----SNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQ 137
           P     + L        N Q   V   +   +    P        +   G    V    Q
Sbjct: 171 PSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQ 230

Query: 138 LVLVNGKSSGDSGRSTPTGD---------------DPTSAKLFVGGLSWQTSSEKLREYF 182
                 +       S P  D               D     +FV  LS  T    L + F
Sbjct: 231 QQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLF 290

Query: 183 GMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G FGAV +V I++D  T + +G+GF++
Sbjct: 291 GPFGAVQNVKIIRDLTTNQCKGYGFVS 317

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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +FV G  + TS E++  YFS FG V   +M    + K    +  V F+++E VD +    
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMNVIM---DKDKGV--YAIVEFDSKEGVDKVLSEP 59

Query: 312 FHMIKNKKVECKKAQ 326
            H +   ++  +  +
Sbjct: 60  QHTLNGHRLRVRPRE 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 15/52 (28%), Positives = 29/52 (55%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
           +FVG +S D   + +   F ++G++    +  D  + R +GFG+V F ++E 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEA 52

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

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 15/52 (28%), Positives = 32/52 (61%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
           +++VG +S++   + +R+ F  FG +  + +  DP+T + +GF F+ +  PE
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPE 53

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

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 23/45 (51%), Positives = 29/45 (64%), Gaps = 4/45 (8%)

Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           E + EYFG FG V DV I   P  Q+ R FGF+TF   ETV+++L
Sbjct: 14  EDVSEYFGQFGPVLDVRI---PYQQK-RMFGFVTFENAETVKRIL 54

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

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
           IFV  +  D     +   FS FG V    ++ D  T + +G+GFVT  N EE    I  +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

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

 Score = 43.5 bits (102), Expect = 6e-06
 Identities = 17/47 (36%), Positives = 33/47 (70%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           +FVG LS + +++ ++  F  FG ++D  ++KD  T +S+G+GF++F
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 13/50 (26%), Positives = 34/50 (68%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           I++GG+  + +  ++   FSQ+G++ +  ++ D++T + +GF F+ +E++
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQ 61

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

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+VG L  + + + L++ F + G V +V I+ D    +   +GF+ + +    E  L+  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQ-- 57

Query: 224 IHTLDGKKI 232
             TL+G++I
Sbjct: 58  --TLNGRQI 64

This subgroup corresponds to the RRM1 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 = 74

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 15/51 (29%), Positives = 34/51 (66%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +++ G+  +T+ E+++     FGK+  T  ++D++T + +G+GFV F++ E
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPE 53

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

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV- 222
           ++V  L    + E L+  F  +G V  V + +   T   +GF FI F  PE  +K  K  
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 223 ---PIHTLDGKKIDPKHAT 238
              P    D     PK   
Sbjct: 62  NNPPETATDKPGKFPKTVA 80

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 9/71 (12%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICE 309
           K+FVG +   T++EE++A F ++G V E  ++        + +GFV  E EE   D I  
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 310 IHFHMIKNKKV 320
           ++ +    K++
Sbjct: 53  LNGYEFMGKRI 63

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 9/70 (12%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K++VG L  + +  +L + F  +G +  V + ++P      GF F+ F +P   E     
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDA--- 52

Query: 223 PIHTLDGKKI 232
            +  LDG++I
Sbjct: 53  -VRALDGRRI 61

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 43.4 bits (102), Expect = 8e-06
 Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFV GLS  T+ E L+E F   G++    I+ D  T  S+GFGF+ F+  E   K  K  
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDA-KAAKEA 58

Query: 224 IH--TLDGKKIDPKHATPK 240
           +    +DG K+    A PK
Sbjct: 59  MEDGEIDGNKVTLDFAKPK 77

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 12/71 (16%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+V  L   T+ E+LRE F  +G V  V  +KD        + F+ F E +   K     
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA---- 51

Query: 224 IHTLDGKKIDP 234
           +  ++GK+++ 
Sbjct: 52  MEEMNGKELEG 62

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

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 13/55 (23%), Positives = 29/55 (52%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           +++V  +    S + ++  F  FG +    +  DP T + +G+GFI +  P++ +
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQ 56

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

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

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            +L V  L +  + E L E FG  G V  V I  D  + RS G   + F + E  E+ +K
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

Query: 222 VPIHTLDGKKIDPKH 236
                 +G  +D + 
Sbjct: 60  ----QFNGVLLDGQP 70

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

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF-ENEEVVDHICEIHF 312
           V  ++  T+ ++++  F ++G+V +  +  D+ T+  RGF FV F +  +  D +  +  
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 313 HMI 315
             +
Sbjct: 63  KEL 65

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           +++G ++ D + ++V+ +F    ++    +  D++T   +GFG V F +EE +D
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLD 54

The CD corresponds to the RRM2 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 16/57 (28%), Positives = 30/57 (52%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
             +FVG +S  T+ E ++  FS++G +    ++ D  T   +G+ FV +E+E     
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

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

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
           +++G L      ++L++YF  FG V +V + +   T  S+ +GFI F  PE      K +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 223 PIHTLDGKKI 232
             + L GK +
Sbjct: 62  NNYLLMGKVL 71

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

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +FVGG+S   +  +++  FS+FG V +  ++  +     RGF ++     E
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 19/69 (27%), Positives = 38/69 (55%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++VG + +  ++E+L  +F   G+V  V I+ D  +   +GF +I F++ E+V   L + 
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 224 IHTLDGKKI 232
                G++I
Sbjct: 62  ESLFRGRQI 70

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 22/57 (38%), Positives = 30/57 (52%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           LFV  ++  T  E LR  FG +G + DV +  D  T+R RGF +I F +    E  L
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59

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

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
           +IF+G + +D   +E+     + GK+ E  M+MD     +RG+ FVTF N +E  + I +
Sbjct: 3   EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQ 61

Query: 310 IHFHMIKNKKV 320
           ++ + I+N ++
Sbjct: 62  LNNYEIRNGRL 72

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++V  L +  ++  L + F  +G V  V I+KD  T++S+G  FI F + E   K     
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC---- 59

Query: 224 IHTLDGKKI 232
           +  L+ K++
Sbjct: 60  VKALNNKEL 68

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 41.7 bits (99), Expect = 1e-05
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 9/58 (15%)

Query: 178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK 235
           L + F  FG V  + ++K        GF F+ F+  E  EK     +  L+G     +
Sbjct: 1   LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKA----VQYLNGVLFGGR 49

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

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 18/54 (33%), Positives = 32/54 (59%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           +FVG +  D   EE++ +F   G VE   ++ D++T   +GFG+V F+ ++ V 
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVA 55

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 4/57 (7%)

Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE----NEEVVDH 306
           V G+S  T+  +++  FS++G +    ++ DQ+T R RGF FV FE    ++E ++H
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 19/61 (31%), Positives = 31/61 (50%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           D  + KLFVG +      + LR  F  FG + ++ ++KD  T   +G  F+T+   E+  
Sbjct: 2   DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 218 K 218
           K
Sbjct: 62  K 62

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

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+VG LS+ T+ E++ E F   G +  +++  D  T+   GF F+ +   E  E  +K  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKY- 59

Query: 224 IHTLDGKKID 233
              L+G K+D
Sbjct: 60  ---LNGTKLD 66

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

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

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 9/73 (12%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           ++LFVG L    + E++R+ F  +G   ++ I KD      +GFGFI   E  T+ ++ K
Sbjct: 2   SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRL-ETRTLAEIAK 54

Query: 222 VPIHT--LDGKKI 232
             +    L GK++
Sbjct: 55  AELDNMPLRGKQL 67

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 164 LFVGGLSWQTSSEKLREYF-GMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
           +FVG LS + +   L   F   F +     IM DP+T  SRG+GF+ F++
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSD 53

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +F+  L        L + FG FGAVT+V +++D  T + +GFGF+T    E       + 
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEA----AMA 59

Query: 224 IHTLDGKKIDPK 235
           I +L+G ++  K
Sbjct: 60  IASLNGYRLGDK 71

This subgroup corresponds to the RRM3 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +   L V  L    + E+ +  FG  G +    +++D IT +S G+GF+ + +P   +K 
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 220 LKVPIHTLDGKKIDPK 235
               I+TL+G K+  K
Sbjct: 62  ----INTLNGLKLQTK 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 164 LFVGGLSWQTSSEKLREYF-GMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           +FVG L+   +   L+E F   + +V    ++ DP+T RS+G+GF+ F 
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFG 52

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           +FV  +      +E++  FS+ G++ +  ++ + +  + +G+ +V FENEE V 
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQ 54

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

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVG LS + +   +R  F  FG++ +  +++D   Q SRG  F+TFA  +     +K 
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQ-SRGCAFVTFASRQCALNAIKA 61

Query: 223 PIH--TLDG 229
             H  T++G
Sbjct: 62  MHHSQTMEG 70

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

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 27/61 (44%), Positives = 33/61 (54%), Gaps = 5/61 (8%)

Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMIKNKKVEC 322
           E+V  YF QFG V + V +  QQ    R FGFVTFEN E V  I  + + H I   +V  
Sbjct: 14  EDVSEYFGQFGPVLD-VRIPYQQ---KRMFGFVTFENAETVKRILSKGNPHFICGSRVRV 69

Query: 323 K 323
           K
Sbjct: 70  K 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 9/71 (12%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
           KLFVG L   T+SE+LR  F  +G VT+  ++K+        +GF+   E E  E  +K 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA 52

Query: 222 VPIHTLDGKKI 232
           +  +   GK+I
Sbjct: 53  LNGYEFMGKRI 63

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

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++FVG +  D + EE++  F ++GK  E  +  D      +GFGF+  E   + +
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAE 51

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

>gnl|CDD|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 = 41.8 bits (99), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
           ++VG +    + EE++  FS FG +EE  +  D+      G+ FV F+  E     I  +
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAV 56

Query: 311 HFHMIKNKKVEC 322
           +   I  + V+C
Sbjct: 57  NGTSINGQTVKC 68

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

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L    + +++R  F   G +    +++D +T +S G+GF+ + +PE  EK     
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA---- 59

Query: 224 IHTLDGKKIDPK 235
           I+TL+G ++  K
Sbjct: 60  INTLNGLRLQNK 71

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KV 222
           +FV  L +  + + L++ F   G V    +  D    RS+GFG + F  PE  ++ +   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 223 PIHTLDGKKID 233
             + L+G++++
Sbjct: 60  NGYDLEGRELE 70

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM---KDPITQRSRGFGFITFAEPETVE 217
           +  L+VG L+ + + E L + FG FG +  V IM    +   +R+R  GF+ F      E
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 218 KVLKVPIHTLDGKKI 232
           + L      LDGK +
Sbjct: 61  RALD----ELDGKDV 71

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 17/82 (20%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            +LFVG L    + E+ +E F  +G V++V + K+      +GFGFI        EK   
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKA-- 53

Query: 222 VPIHTLDGKKIDPKHATPKNRP 243
                LDG          K R 
Sbjct: 54  --KAELDGIMR-------KGRQ 66

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

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           P S +LFVG L       +L+E+F  FG V ++ I    +  +   FGF+ F + E V++
Sbjct: 3   PDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62

Query: 219 VL 220
           +L
Sbjct: 63  IL 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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 20/60 (33%), Positives = 33/60 (55%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+V GL    + ++L + F  +G +    I++D +T  SRG GFI F +    E+ +K
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 17/76 (22%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
           +IFVG +  + + E +   FS++   ++  ++ D++T + +G+GFV+F +  + +  + E
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 310 IHFHMIKNKKVECKKA 325
           ++   + N+ ++ +K+
Sbjct: 68  MNGKYVGNRPIKLRKS 83

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 252 IFVGGVSQDTSAEEVKAY--FSQFGKVEETVMLM-DQQTKRHRGFGFVTFENEEVVD 305
           +F+G +  D   +E   Y  FS FG + +T  +M D  T   +GF F+++++ E  D
Sbjct: 4   LFIGNL--DPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASD 58

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

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVDHI 307
           ++V  + ++ + E +KA FS++G V    +   + T   +GF F+ FE  E       H+
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 308 CEIHFHMIKNKKVECKKA 325
                          K  
Sbjct: 62  NNPPETATDKPGKFPKTV 79

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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 45.5 bits (108), Expect = 4e-05
 Identities = 18/104 (17%), Positives = 23/104 (22%), Gaps = 4/104 (3%)

Query: 1   METMALGGAPDHHEQFNGLIPTMNGLVQIPHHPGLV----HLNGPPPPPHQLVKLNGAPQ 56
                    P  + Q     P      Q    P        L    P     ++    P 
Sbjct: 191 FPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPG 250

Query: 57  VNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVL 100
           ++   P       Q   QP Q Q QPP        P        
Sbjct: 251 LSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNA 294

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 19/47 (40%), Positives = 29/47 (61%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           +FV  L+       L + FG FGAVT+V +++D  T + +GFGF+T 
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTM 52

This subgroup corresponds to the RRM3 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 = 86

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 19/47 (40%), Positives = 29/47 (61%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           +FV  LS  +    L + FG FGAV +V +++D  T + +GFGF+T 
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTM 52

This subgroup corresponds to the RRM3 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 it also regulates the neurite elongation and morphological differentiation. HuD specifically bound 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 = 86

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVD 305
           + ++V G+S  T A ++K  FS++GKV    ++ + ++   R +GFVT    E     ++
Sbjct: 2   RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61

Query: 306 HI--CEIHFHMI 315
           H+   E+H  MI
Sbjct: 62  HLHRTELHGRMI 73

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. 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. Length = 76

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

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 17/55 (30%), Positives = 30/55 (54%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           K+FVG V +  + +EV+  F + G V E  ++ D++T   +G  FV +   +  D
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEAD 55

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

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 21/76 (27%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
           +FV  ++ DT +E+++  F ++G + +  + +D  T+R RGF +V FE+  +  D +  +
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 311 HFHMIKNKKVECKKAQ 326
               I  +++E + AQ
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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           D  S  +FVG LS   + E+L E F   G + +V ++K      +  F FI F   +   
Sbjct: 2   DKYS--IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRA--NHTNAFAFIKFEREQAAA 57

Query: 218 KVLK 221
           + ++
Sbjct: 58  RAVE 61

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

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 265 EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECK 323
           +++  F QFG + +  ++ +++  +  GFGFVTF N    D   E +H  +++ +K+E  
Sbjct: 16  DLRQMFGQFGPILDVEIIFNERGSK--GFGFVTFANSADADRAREKLHGTVVEGRKIEVN 73

Query: 324 KA 325
            A
Sbjct: 74  NA 75

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.2 bits (95), Expect = 6e-05
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 8/62 (12%)

Query: 266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHM--IKNKKVECK 323
           +   FS FG VE+  +L     K+  GF FV F  EE  +   + + +      + +   
Sbjct: 1   LYKLFSPFGNVEKIKLL-----KKKPGFAFVEFSTEEAAEKAVQ-YLNGVLFGGRPLRVD 54

Query: 324 KA 325
            +
Sbjct: 55  YS 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 6/50 (12%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           ++FVG +  D + EE K  FS++G+V E  +       + +GFGF+  + 
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDT 46

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

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKV 219
           + +FV  L ++   +KL+E F M G V    I++D    +SRG G +TF +P E V+ +
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTFEQPIEAVQAI 58

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

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

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
           +FVG + +D   +E+   F + G + E  ++MD     +RG+ FVT+ N E     + ++
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVKQL 62

Query: 311 HFHMIKNKK 319
           H + I+  K
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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 3/53 (5%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K +FV G+S+DT+ E +K  F   G +   ++  D+ T   +GFGFV F +EE
Sbjct: 1   KTLFVKGLSEDTTEETLKESFD--GSIAARIV-TDRDTGSSKGFGFVDFSSEE 50

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+V GL    + ++L   F  +G +    I+ D +T  SRG GFI F +    E    
Sbjct: 1   ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAE---- 56

Query: 222 VPIHTLDGKK 231
             I  L+G  
Sbjct: 57  RAIKALNGTI 66

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 9/75 (12%)

Query: 163 KLFVGGLSWQTSSEK----LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
            +FV G       +     L E+F   G +T V I  D  T  S+GF +I F   + VEK
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 219 VLKVPIHTLDGKKID 233
            L+     LDG  + 
Sbjct: 61  ALE-----LDGSDLG 70

This subfamily corresponds to the RRM2 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 = 79

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

 Score = 40.6 bits (95), Expect = 8e-05
 Identities = 15/54 (27%), Positives = 32/54 (59%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++VG V   ++AEE++A+FS  G +    +L D+ +   +G+ ++ F   + V+
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVE 55

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

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
           KL V  + ++ + ++LRE F  FG V  V + K       RGF F+ F   +
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQ 52

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 7/51 (13%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           RT  +FV  ++ +   EE++A F QFG +           K HRGF  V++
Sbjct: 2   RT--LFVRNINSNVEDEELRALFEQFGDIRTLYT----ACK-HRGFIMVSY 45

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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 9/73 (12%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
           +++V     DTS   ++  FS +G V+E  M+          F FV FE+ E  +     
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 310 IHFHMIKNKKVEC 322
           +H  ++ N  +  
Sbjct: 53  VHGKVLNNNPLYV 65

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

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
            ++V  +      E ++  FS FG +    ++ D++  R +GFGFV F + EE    + E
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTE 61

Query: 310 IHFHMIKNK 318
           ++  +I  K
Sbjct: 62  MNGRIIGGK 70

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 40.3 bits (94), Expect = 9e-05
 Identities = 18/60 (30%), Positives = 35/60 (58%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++FVG +      ++L   F   G + D+ +M DP++ ++RG+ FITF   E  ++ +K+
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62

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|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 8/55 (14%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG-FGFVTFENEE 302
            K  F+ GV  D    +++ YF QFGK +  ++        HR   GFV FE  E
Sbjct: 2   IKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIV-------NHRAKCGFVRFETRE 49

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 5/55 (9%)

Query: 261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHM 314
           T+ E+++  FS+FGK++   ++ D++T     + F+ FE +E     CE  +F M
Sbjct: 15  TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED----CEEAYFKM 65

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 14/52 (26%), Positives = 32/52 (61%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
           SA +++GGL ++ +   +   F  +G + D+ +++D  T +S+GF F+ + +
Sbjct: 9   SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++VG V    +AEE++A+F   G V    +L D+ +   +GF ++ F ++E V 
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 55

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 33/52 (63%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           R   ++V G+ +  + +E++  FSQ+G++  + +L+DQ T   RG GF+ F+
Sbjct: 1   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 52

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 9/71 (12%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           KIFVG V +DTS EE++A F  +G V  +  +M Q       F FV    E   D  I E
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAV-LSCAVMRQ-------FAFVHLRGEAAADRAIEE 53

Query: 310 IHFHMIKNKKV 320
           ++   +  +K+
Sbjct: 54  LNGRELHGRKL 64

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

>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 9/50 (18%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEE-TVMLMDQQTKRHRG--FGFVTF 298
           I+VG +  DT+  E++  F  FG++EE TV L      R  G  +GF+T+
Sbjct: 5   IYVGKIRPDTTRTELRDRFEVFGEIEECTVNL------RDDGDSYGFITY 48

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

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

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 17/81 (20%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           +LFVG L    + E  ++ F  +G  ++V I +D      RGFGFI   E  T+ ++ K 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRL-ESRTLAEIAKA 55

Query: 223 PIHTLDGKKIDPKHATPKNRP 243
               LDG  +       KNRP
Sbjct: 56  ---ELDGTIL-------KNRP 66

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

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 15/66 (22%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 265 EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK 324
           ++  +FS+ GKV +   + D+ ++R +G  +V F + E V     +   M+  + +    
Sbjct: 105 DLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPI---I 161

Query: 325 AQPKEA 330
            Q  +A
Sbjct: 162 VQSSQA 167

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 14/51 (27%), Positives = 32/51 (62%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           + VG ++++ + + +K  FS +G V++  + +D++    RG+ +V FE+ E
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPE 51

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           +RT  +FVG +    + E +   F Q G +E   +  D   K  + F FVTF++E  V +
Sbjct: 1   DRT--LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP-KSFAFVTFKHEVSVPY 57

Query: 307 ICEI 310
             ++
Sbjct: 58  AIQL 61

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           LFVG L  +   E L E F   G +T V I KD    + + FGF+ F   E+V
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESV 55

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           +FVGGL    + ++LR  FG FG +  V I   P     +G GF+ F      E  +
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PP---GKGCGFVQFVHRAAAEAAI 54

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

>gnl|CDD|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 = 39.4 bits (92), Expect = 2e-04
 Identities = 15/51 (29%), Positives = 33/51 (64%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +FVG +  + + E++K  FS+ G V    ++ D++T + +G+GF  ++++E
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQE 51

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++FVG +      ++L   F   G + D+ +M DP+T  +RG+ F+TF   E  ++ +K+
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++ G         +VK  F   G V +  ML    ++  +   F+TFEN E   
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQ 51

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

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE-NEEVVDHICE 309
           KIFVG VS   +++E++  F +FG+V E   + D        + FV  E  EE +  I  
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEA 53

Query: 310 IHFHMIKNKKV 320
           ++   +K +++
Sbjct: 54  LNGKEVKGRRI 64

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

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++V G  +D + ++++ +F +FGKV   + +     K+ +G  FV F+ EE   
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKV-NNIRMRRDLDKKFKGSVFVEFKTEEDAK 54

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

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

 Score = 42.2 bits (99), Expect = 3e-04
 Identities = 28/94 (29%), Positives = 42/94 (44%), Gaps = 6/94 (6%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
           P+ D    A L+V GL    +  +L   F  FG +    I+ D +T  S+G GFI F + 
Sbjct: 82  PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKR 141

Query: 214 ETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGN 247
           +  ++ +K    TL+G    P   T     K  N
Sbjct: 142 DEADRAIK----TLNGTT--PSGCTEPITVKFAN 169

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           ++ V  +    +  ++K  FS FG V E  +       + +GF FV F +
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTS 49

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 13/44 (29%), Positives = 28/44 (63%)

Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           Q+ + +E+++ FS  G++E   ++ D+ T +  G+GFV + + E
Sbjct: 11  QNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPE 54

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

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++V G+ +  + +E++  FSQ+G++  + +L DQ T   RG GF+ F+   
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRI 53

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|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 = 25/94 (26%), Positives = 44/94 (46%), Gaps = 21/94 (22%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
            K+ V  V  + + +E++  FS FG+V+ +V L  +    HRGF FV F  ++       
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVK-SVRLPKKFDGSHRGFAFVEFVTKQ------- 52

Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLLVGKRVIL 343
                      E + A   EA+++  L G+ ++L
Sbjct: 53  -----------EAQNA--MEALKSTHLYGRHLVL 73

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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           +L+V      TS   +RE F  +GAV +V ++          F F+ F   E+  +
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIR 48

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 32/52 (61%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++FVG + +D   +E+   F + G + +  ++MD  + ++RG+ F+TF  +E
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKE 54

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

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           ++FVG +  D + E+ K  F ++G+  E  +       R RGFGF+  E+  + +
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAE 51

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

>gnl|CDD|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 = 38.6 bits (90), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 30/52 (57%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           +FVG + ++ + E+L++ F   G V    ++ D  T + +G+GF  + + ET
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQET 52

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 11/70 (15%), Positives = 29/70 (41%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           + + G+    + E+++ +FS      + + ++     R  G  +V F + E        H
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 312 FHMIKNKKVE 321
            + +  + +E
Sbjct: 62  NNKMGGRYIE 71

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

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

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           P S +LFVG L       +L+E+F  +G V ++ I       +   FGF+ F + E V+K
Sbjct: 1   PDSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQK 57

Query: 219 VL 220
           +L
Sbjct: 58  IL 59

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|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 = 38.8 bits (91), Expect = 3e-04
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 163 KLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           +L V  L    +  +L+E+F    G +TDV +++     +SR   FI +   E  +K   
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAKD 60

Query: 222 V 222
            
Sbjct: 61  Y 61

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|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 5/84 (5%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMK---DPITQRSRGFGFITFAEPETVEK 218
           A ++VG  SW T+ ++L +     G V DV+ +K   +    +S+G+  +  A   +V K
Sbjct: 2   AAVYVGNFSWWTTDQQLIQVIRSVG-VKDVVELKFAENRANGQSKGYAEVVVASENSVHK 60

Query: 219 VLK-VPIHTLDGKKIDPKHATPKN 241
           +L+ +P   L+G+K+D + AT +N
Sbjct: 61  LLELLPGKVLNGEKVDVRPATRQN 84

This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 90

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

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 4/57 (7%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF----ENEEVV 304
           ++V G+ +  S +E++  FSQ+G++  + +L+DQ T   RG GF+ F    E EE +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 7/55 (12%)

Query: 252 IFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +++  +++    +E+K    A FSQFG V + V     +T + RG  FV F++ E
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVAS---KTLKMRGQAFVVFKDVE 53

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

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           QD + EE+++ F   G +E   ++ D+ T +  G+GFV + +E 
Sbjct: 10  QDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDEN 53

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

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLFVG +    + +++R  F   G V +V I+KD  T   +G  F+ ++  +  ++    
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA--- 57

Query: 223 PIHTLDGKKIDPKHATP 239
            I  L  ++  P  A+P
Sbjct: 58  -IRALHNQRTLPGGASP 73

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

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+V GL    + ++L + F  +G +    I+ D +T  SRG GFI F +    E+ +K
Sbjct: 3   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

Query: 222 VPIHTLDGKKIDPKHAT 238
                L+G+K  P  A 
Sbjct: 63  ----GLNGQK--PSGAA 73

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 13/70 (18%), Positives = 34/70 (48%), Gaps = 12/70 (17%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++++G L ++     +  +F  +G + ++ +          GFGF+ F +P   +     
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDA--- 49

Query: 223 PIHTLDGKKI 232
            ++ L+GK++
Sbjct: 50  -VYELNGKEL 58

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

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L    + ++LR  F   G V    +++D +   S G+GF+ +   +  E+     
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERA---- 59

Query: 224 IHTLDGKKIDPK 235
           I+TL+G ++  K
Sbjct: 60  INTLNGLRLQSK 71

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 5/49 (10%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEE-TVMLMDQQTKRHRGFGFVTFE 299
           I+VG +  DT+  E++  F  FG++EE T+   D        +GFVT+ 
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN----YGFVTYR 49

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

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

 Score = 39.0 bits (90), Expect = 4e-04
 Identities = 17/52 (32%), Positives = 33/52 (63%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           R   ++V G+ +  + +E++  FSQ+G++  + +L+DQ T   RG GF+ F+
Sbjct: 4   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 55

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             +FVG + +  S + ++    + GKV     + D  T + + FGF  FE+ E
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPE 53

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP----ETVEKV 219
           + + GLS  T+ +++R +F  FG + +  +  DP T +S G   +TF           + 
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 220 LKVPIHTLDGKKIDPK 235
            K  +  L+G++I  K
Sbjct: 61  AKAAVDGLNGRRIGGK 76

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 19/47 (40%), Positives = 26/47 (55%)

Query: 174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           + E LRE F  FG +  V I+KD  T  S+GFG++ F +P      L
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           KLFVG LS Q + + +R  F  FG + +  I++ P    S+G  F+ F+
Sbjct: 3   KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN-SKGCAFVKFS 50

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

>gnl|CDD|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 = 38.0 bits (89), Expect = 5e-04
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 6/48 (12%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           ++VG L    + E+L+  F  FGA+ +V + KD      +G+ F+ F 
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFD 44

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

 Score = 41.8 bits (98), Expect = 5e-04
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 6/91 (6%)

Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
            N K+      ST   D     ++++G L      ++++E    FG +    ++KD  T 
Sbjct: 277 DNAKNVEKLVNSTTVLDSKD--RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATG 334

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKK 231
            S+G+ F  + +P   +    V I  L+GK 
Sbjct: 335 LSKGYAFCEYKDPSVTD----VAIAALNGKD 361

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           +K+F+G VS+  +  +++  FS FG++EE  +L        RG  FVTF
Sbjct: 2   RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTF 49

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

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKV 219
           + +FV  L ++   +KL+E F + G V    I +D    +SRG G +TF +P E V+ +
Sbjct: 1   STIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDK-DGKSRGMGTVTFEQPIEAVQAI 58

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

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

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 19/76 (25%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
           +FV  V+  T  E+++  F ++G + +  + +D  T+R RGF ++ FE+  +  D +  +
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 311 HFHMIKNKKVECKKAQ 326
           +   +  +++E + AQ
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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 16/82 (19%), Positives = 18/82 (21%), Gaps = 2/82 (2%)

Query: 24  NGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAP--QVNTSPPQNAILHQQPTPQPQQQQQQ 81
                +            PPPP Q  +    P       PPQN        PQ Q     
Sbjct: 238 QQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLP 297

Query: 82  PPQPQPRDLQPNSNNQLVLVNG 103
           PPQ                   
Sbjct: 298 PPQQPQLLPLVQQPQGQQRGPQ 319

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI-TQRSRGFGFITF 210
           K+ V  + ++ + ++LRE F  FG +  V + K    T   RGFGF+ F
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDF 50

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

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 12/69 (17%)

Query: 179 REYFGMFGAVTDV---LIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDG-----K 230
            E+  +F AV  V    I++D  T  S GFGF+ +   E  ++     I TL+G     K
Sbjct: 15  EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA----IRTLNGLQLQNK 70

Query: 231 KIDPKHATP 239
           +I   +A P
Sbjct: 71  RIKVAYARP 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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 37.4 bits (87), Expect = 8e-04
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 13/83 (15%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LF+G L   T+   LRE F  FG + D+ I K      +  + FI +A+  +V K ++  
Sbjct: 5   LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQG---GNPAYAFIQYADIASVVKAMR-- 59

Query: 224 IHTLDGKKIDPKHATPKNRPKIG 246
              +DG+ +        NR K+G
Sbjct: 60  --KMDGEYLG------NNRVKLG 74

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

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

 Score = 37.2 bits (87), Expect = 9e-04
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHIC 308
           K ++V  +   T+ E+++  FS++G+VE    + D        + FV FE  ++ V  + 
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAME 53

Query: 309 EIHFHMIKNKKVECKKAQP 327
           E++   ++   +E   A+P
Sbjct: 54  EMNGKELEGSPIEVSLAKP 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|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 = 0.001
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGL    S ++++E    FG +    ++KD  T  S+G+ F  + +P     V   
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDP----SVTDQ 57

Query: 223 PIHTLDGKKI 232
            I  L+G ++
Sbjct: 58  AIAGLNGMQL 67

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           IFV  +    + +++K  F + G V    +  D    R +GFG V FE+ E      E+
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEM 58

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++VG + + +++E+L  +F   G +  V I+ D  +   +G+ +I FA  ++VE  + + 
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61

Query: 224 IHTLDGK--KIDPK 235
             +  G+  K+ PK
Sbjct: 62  ESSFRGRVIKVLPK 75

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

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +IFVG + +D   +E+   F + G + +  ++MD  T  +RG+ FVTF  +E
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKE 54

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 8/70 (11%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++ G          ++  F   G V  V +    +++  +   FITF   E  +      
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTM----LSRTVQPHAFITFENLEAAQLA---- 53

Query: 224 IHTLDGKKID 233
           I TL+G  +D
Sbjct: 54  IETLNGASVD 63

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

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 7/62 (11%)

Query: 164 LFVGGLSWQTSSEKLR----EYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           L++  L+ +   ++L+      F  FG V D++  K   T + RG  F+ F + E+    
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATNA 58

Query: 220 LK 221
           L+
Sbjct: 59  LR 60

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

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 8/51 (15%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           ++++G +       +V+ +F  +G++ E  +          GFGFV FE+ 
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDP 43

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           ++FV  + +  + E+++  F +FG +E   ++ D+ T   +GFG+V 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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ--QTKRHRGFGFVTF 298
           KI V  +  + + +E++  FS FG+++ TV L  +   T  HRGFGFV F
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELK-TVRLPKKMTGTGSHRGFGFVDF 50

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

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
           +VG L   T++++L E+F   G V  V +  D  TQ +R + F+ FAE  +V   LK+  
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTR-YAFVEFAEQTSVINALKLNG 65

Query: 225 HTLDGKKIDPKHAT 238
               G+ +   H+ 
Sbjct: 66  AMFGGRPLKVNHSN 79

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

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 5/61 (8%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM--KDPITQRSRGFGFITFAEPETVEKVL 220
           +L V  L      +KLR+ F  FG +TDV +   KD      R FGF+ +   E  +K L
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKF---RKFGFVGYKTEEEAQKAL 58

Query: 221 K 221
           K
Sbjct: 59  K 59

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 11/74 (14%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI------TQRSRGFGFITFAEPETV 216
           ++++  LS+ +S E L E+   F  V+ VLI    +        R  G  +  F+ PE  
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPVS-VLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 217 EKVLKVPIHTLDGK 230
           EKV+K     L+GK
Sbjct: 60  EKVVK----DLNGK 69

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

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 18/51 (35%), Positives = 25/51 (49%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           IF+  + QD     +   F  FG V    ++ D  T + +GFGFVT  N E
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYE 54

This subgroup corresponds to the RRM3 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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 18/49 (36%), Positives = 25/49 (51%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           IFV  +S D+    +   F  FG V    ++ D  T + +GFGFVT  N
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTN 54

This subgroup corresponds to the RRM3 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 it also regulates the neurite elongation and morphological differentiation. HuD specifically bound 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 = 86

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

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+V GL    S +++ + F  +G +    I+ D +T  SRG GFI F +    E+ +K
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61

Query: 222 VPIHTLDGKK 231
                L+G+K
Sbjct: 62  ----GLNGQK 67

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 = 37.1 bits (85), Expect = 0.002
 Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 6/86 (6%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+V GL    + ++L + F  +G +    I+ D +T  SRG GFI F +    E+ +K
Sbjct: 6   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

Query: 222 VPIHTLDGKKIDPKHATPKNRPKIGN 247
                L+G+K  P  AT     K  N
Sbjct: 66  ----GLNGQK--PPGATEPITVKFAN 85

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           + LRE F  FG + D+ ++KD  T+ S+G  ++ FA
Sbjct: 17  DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 52

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|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +++G +    +  E+K  FS FG++EE  +    +      +GFVT+   E
Sbjct: 5   VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGD---NYGFVTYRYTE 52

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 11/73 (15%)

Query: 166 VGGLSWQTSSEKLREYFGMF-----GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           V GL    S +KL  YF        G VT V  +++       G   +TFA+ +  E+V+
Sbjct: 5   VAGLPETVSDDKLELYFENKRRSGGGDVTRVQYLREK------GSALVTFADFKVAERVV 58

Query: 221 KVPIHTLDGKKID 233
           K   H L+G ++ 
Sbjct: 59  KQKKHPLNGTQLS 71

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

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV---- 216
           +  +F   L+ +     L E+F   G V DV ++ D  ++RS+G  ++ F +  +V    
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60

Query: 217 ----EKVLKVPI 224
               ++VL VPI
Sbjct: 61  GLTGQRVLGVPI 72

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>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 = 36.6 bits (85), Expect = 0.002
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
            K+FV G+    + EE++  F + G V+  V L+  ++ + +G  +V +ENE
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKS-VRLVTNRSGKPKGLAYVEYENE 53

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 12/70 (17%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++F+G L+     + +  +F  +G + D+ +         RGFGF+ F +P   +     
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDA--- 49

Query: 223 PIHTLDGKKI 232
            ++ LDGK++
Sbjct: 50  -VYELDGKEL 58

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

>gnl|CDD|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 = 36.6 bits (85), Expect = 0.002
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           RT  I VGG+    S +++K +FS  G+V    +  D+Q      F FV F + E
Sbjct: 1   RT--IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAE 51

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 176 EKLREYFGMFGAVTDVLI-MKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP 234
           + LR+ F  FG    V I M    T +++G+ F+ FA PE  ++ +K     L+G K+D 
Sbjct: 22  KVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVK----ALNGYKLDK 77

Query: 235 KH 236
           KH
Sbjct: 78  KH 79

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

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 16/74 (21%)

Query: 164 LFVGGLSWQTSSEKLR----EYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           LFVG L+     ++L+    E+F     AV DV I        S+ FG++ F   E +EK
Sbjct: 3   LFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRI------GSSKKFGYVDFESAEDLEK 56

Query: 219 VLKVPIHTLDGKKI 232
            L+     L GKK+
Sbjct: 57  ALE-----LTGKKL 65

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 9/54 (16%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           L+VGGL   TS  +L   F  FGA+  +           R + +I +   E++E
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI------DYDPGRNYAYIEY---ESIE 45

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 13/51 (25%), Positives = 27/51 (52%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           + VG +  + + E+ +   S FG VE   ++  + T   +G+GFV + ++ 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKA 52

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K++VG +    +  E++  F ++G +  +V +     +   GF FV FE+  
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPL-RSVWV----ARNPPGFAFVEFEDPR 47

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYF-SQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           IFVG +S + +  ++ + F S+F   +   ++ D  T   RG+GFV 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           IFVG ++ D +   ++  F   +  V    ++MD  T R +G+GFV F +E+
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDED 55

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 15/48 (31%), Positives = 30/48 (62%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           ++V G+ +  + +E++A FS +G++  + +L D  T   RG GF+ F+
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFD 50

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|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 = 36.2 bits (84), Expect = 0.003
 Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
            VGG+    S + L+E+F   G VT V +  D   Q S  F F+ FA+ E+    L +  
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDR--QHSARFAFVEFADAESALSALNLSG 61

Query: 225 HTLDGKKI 232
             L G  +
Sbjct: 62  TLLGGHPL 69

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ---QTKRHRGFGFVTFENEEVVDH- 306
           ++++G +    +   +   FS++GK+++   L  +      + RG+ FVTFE +E  +  
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 307 ICEIHFHMIKNKK 319
           +  ++      KK
Sbjct: 61  LKSLNGKTALGKK 73

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|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 = 36.3 bits (84), Expect = 0.003
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR--SRGFGFITF 210
           K+FVG +    S + LRE F  +GAV  + +++D       S+G  F+TF
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++FVG + +D   +E+   F + GK+ E  ++M + +  +RG+ FV +  +E
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMM-EFSGENRGYAFVMYTTKE 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|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 8/69 (11%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV------- 216
           +F   L+ +     L ++F   G V DV I+ D  ++RS+G  ++ F E ++V       
Sbjct: 4   VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT 63

Query: 217 -EKVLKVPI 224
            +++L VPI
Sbjct: 64  GQRLLGVPI 72

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 9/77 (11%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR-----SRGFGFITFAEPETV 216
           A LFV  L++ T+++ L + F          +   P  +R     S GFGF+ F   E  
Sbjct: 1   ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQA 60

Query: 217 EKVLKVPIHTLDGKKID 233
           +  LK     +DG  +D
Sbjct: 61  QAALKA----MDGFVLD 73

This subfamily corresponds to the RRM4 of MRD1which 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 = 84

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           ++FVG + +D   +E+   F   G++ E  ++MD   K +RG+ FV +
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGK-NRGYAFVMY 49

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 187 AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI 232
            V  V I+++ +T    G+ F+ FA+  T E+ L    H L+GK I
Sbjct: 26  TVLSVKIIRNKLTGGPAGYCFVEFADEATAERCL----HKLNGKPI 67

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

>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 18/86 (20%)

Query: 168 GLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTL 227
           GL +  + + + ++F     V D +++      R  G  ++ FA PE   K L       
Sbjct: 8   GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALL------ 61

Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIF 253
                       K+R +IGNR  ++F
Sbjct: 62  ------------KHREEIGNRYIEVF 75

This subfamily corresponds to the RRM2 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	398
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0148|consensus	321		100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0144|consensus	510		99.98
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.98
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
KOG0145|consensus	360		99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
KOG0145|consensus	360		99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0117|consensus	506		99.96
KOG0131|consensus	203		99.96
KOG0124|consensus	544		99.95
KOG0127|consensus	678		99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0127|consensus	678		99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG4205|consensus	311		99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0109|consensus	346		99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0123|consensus	369		99.92
KOG0148|consensus	321		99.91
KOG0123|consensus	369		99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.9
KOG0146|consensus	371		99.88
KOG0110|consensus	725		99.88
KOG0147|consensus	549		99.88
KOG0144|consensus	510		99.87
KOG4211|consensus	510		99.85
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.81
KOG0105|consensus	241		99.79
KOG4206|consensus	221		99.76
KOG0147|consensus	549		99.76
KOG4212|consensus	608		99.76
KOG1548|consensus	382		99.73
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.72
KOG0124|consensus	544		99.71
KOG0149|consensus	247		99.69
KOG0149|consensus	247		99.67
KOG0125|consensus	376		99.67
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.67
KOG0122|consensus	270		99.66
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.65
KOG0110|consensus	725		99.65
KOG0106|consensus	216		99.64
KOG0126|consensus	219		99.63
KOG1457|consensus	284		99.62
PLN03120	260	nucleic acid binding protein; Provisional	99.62
KOG0113|consensus	335		99.61
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.61
KOG0125|consensus	376		99.59
KOG0129|consensus	520		99.58
KOG0121|consensus	153		99.58
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.57
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.57
KOG1190|consensus	492		99.56
KOG0122|consensus	270		99.56
KOG1365|consensus	508		99.55
KOG0121|consensus	153		99.54
KOG0120|consensus	500		99.54
KOG0126|consensus	219		99.54
PLN03120	260	nucleic acid binding protein; Provisional	99.54
PLN03121	243	nucleic acid binding protein; Provisional	99.53
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.52
KOG4207|consensus	256		99.52
KOG0114|consensus	124		99.51
KOG0117|consensus	506		99.51
KOG0113|consensus	335		99.5
KOG0107|consensus	195		99.5
KOG4212|consensus	608		99.5
KOG0130|consensus	170		99.48
PLN03121	243	nucleic acid binding protein; Provisional	99.47
PLN03213	759	repressor of silencing 3; Provisional	99.47
KOG0146|consensus	371		99.46
KOG0107|consensus	195		99.46
KOG0114|consensus	124		99.46
smart00362	72	RRM_2 RNA recognition motif.	99.44
KOG4207|consensus	256		99.43
smart00360	71	RRM RNA recognition motif.	99.43
KOG0108|consensus	435		99.41
KOG0108|consensus	435		99.41
KOG0111|consensus	298		99.39
PLN03213	759	repressor of silencing 3; Provisional	99.39
KOG0120|consensus	500		99.38
KOG0131|consensus	203		99.38
smart00362	72	RRM_2 RNA recognition motif.	99.38
KOG1456|consensus	494		99.37
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.36
KOG1190|consensus	492		99.36
KOG0226|consensus	290		99.35
KOG0111|consensus	298		99.34
smart00360	71	RRM RNA recognition motif.	99.34
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.33
KOG1365|consensus	508		99.33
KOG4205|consensus	311		99.3
KOG4210|consensus	285		99.3
KOG4307|consensus	944		99.29
smart00361	70	RRM_1 RNA recognition motif.	99.28
KOG4211|consensus	510		99.28
KOG0109|consensus	346		99.27
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.26
KOG0130|consensus	170		99.26
KOG0415|consensus	479		99.25
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.24
KOG0105|consensus	241		99.22
KOG4208|consensus	214		99.2
KOG4454|consensus	267		99.19
KOG0153|consensus	377		99.19
smart00361	70	RRM_1 RNA recognition motif.	99.15
KOG0128|consensus	881		99.15
KOG0132|consensus	894		99.09
KOG1456|consensus	494		99.07
KOG4206|consensus	221		99.07
KOG0132|consensus	894		99.07
KOG0112|consensus	975		99.03
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.01
KOG4208|consensus	214		99.0
KOG0153|consensus	377		98.95
KOG0415|consensus	479		98.95
KOG0116|consensus	419		98.9
KOG0226|consensus	290		98.88
KOG4661|consensus	940		98.88
KOG4660|consensus	549		98.82
KOG4307|consensus	944		98.79
KOG0533|consensus	243		98.79
KOG0116|consensus	419		98.75
KOG4661|consensus	940		98.75
KOG4209|consensus	231		98.71
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.69
KOG4209|consensus	231		98.66
KOG1457|consensus	284		98.62
KOG0533|consensus	243		98.6
KOG1548|consensus	382		98.56
KOG0128|consensus	881		98.46
KOG4660|consensus	549		98.46
KOG4676|consensus	479		98.45
KOG0106|consensus	216		98.44
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.43
KOG2193|consensus	584		98.41
KOG4454|consensus	267		98.39
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.26
KOG0151|consensus	877		98.21
KOG0151|consensus	877		98.19
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.12
KOG1995|consensus	351		98.01
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.89
KOG4849|consensus	498		97.88
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.81
KOG1855|consensus	484		97.76
KOG4210|consensus	285		97.76
KOG1995|consensus	351		97.73
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.67
KOG4849|consensus	498		97.64
KOG1996|consensus	378		97.63
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.62
KOG3152|consensus	278		97.53
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.51
KOG3152|consensus	278		97.49
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.41
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.35
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.34
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.31
KOG2314|consensus	698		97.3
KOG0115|consensus	275		97.29
KOG0129|consensus	520		97.27
KOG2314|consensus	698		97.15
KOG1855|consensus	484		97.07
KOG2202|consensus	260		96.79
KOG2253|consensus	668		96.76
KOG4676|consensus	479		96.41
KOG0112|consensus	975		96.36
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.34
KOG1924|consensus	1102		96.23
KOG0115|consensus	275		96.21
KOG2135|consensus	526		96.2
KOG1996|consensus	378		96.17
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.09
KOG2416|consensus	718		96.08
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.77
KOG2202|consensus	260		95.76
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.69
KOG2068|consensus	327		95.45
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.43
KOG2416|consensus	718		95.22
KOG4285|consensus	350		95.08
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.03
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	94.97
KOG2068|consensus	327		94.96
KOG4285|consensus	350		94.94
KOG2135|consensus	526		94.86
KOG2193|consensus	584		94.74
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.46
KOG2591|consensus	684		94.38
KOG2591|consensus	684		94.36
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.3
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.05
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.9
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.41
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.28
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.27
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	93.17
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.71
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	90.61
KOG0804|consensus	493		90.13
KOG3702|consensus	681		89.36
KOG2891|consensus	445		89.33
KOG0804|consensus	493		88.81
KOG2253|consensus	668		88.32
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	88.15
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	84.11
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	83.91
TIGR02542	145	B_forsyth_147 Bacteroides forsythus 147-residue re	83.69
KOG4483|consensus	528		83.27
KOG4410|consensus	396		83.16
KOG2318|consensus	650		82.86
KOG4574|consensus	1007		81.95
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	80.57

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=2.9e-35  Score=275.57  Aligned_cols=174  Identities=18%  Similarity=0.364  Sum_probs=155.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||.++||++|+++|+.||.|++|+|++|+.+++++|||||+|.++++|++||+ +++..+.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            445578999999999999999999999999999999999999999999999999999999999997 8999999999999


Q ss_pred             CCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCc
Q psy6490         235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFH  313 (398)
Q Consensus       235 ~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~  313 (398)
                      .++.+...   ....++|||+|||.++||++|+++|++||.|++|+|++|+.++++||||||+|++.++|++|+ +||+.
T Consensus       182 ~~a~p~~~---~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  258 (346)
T TIGR01659       182 SYARPGGE---SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV  258 (346)
T ss_pred             eccccccc---ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            98865432   234568999999999999999999999999999999999999999999999999977776555 69999


Q ss_pred             eeCC--EEEEEEecCchHHHh
Q psy6490         314 MIKN--KKVECKKAQPKEAVQ  332 (398)
Q Consensus       314 ~i~g--~~i~v~~a~~k~~~~  332 (398)
                      .|.+  +.|+|+|+..+...+
T Consensus       259 ~~~g~~~~l~V~~a~~~~~~~  279 (346)
T TIGR01659       259 IPEGGSQPLTVRLAEEHGKAK  279 (346)
T ss_pred             ccCCCceeEEEEECCcccccc
Confidence            8866  789999998765443

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=100.00  E-value=7.1e-35  Score=286.32  Aligned_cols=169  Identities=21%  Similarity=0.483  Sum_probs=151.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+||++++++++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|++|++ +++..++|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            56899999999999999999999999999999999999999999999999999999999997 89999999999998654


Q ss_pred             CCCCC--------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHH
Q psy6490         239 PKNRP--------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE  309 (398)
Q Consensus       239 ~~~~~--------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~  309 (398)
                      .....        ......++|||+||+.++++++|+++|+.||.|++|+|.+|+.++++||||||+|++.++|.+ +.+
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            32211        112345789999999999999999999999999999999999999999999999999776655 557


Q ss_pred             HCCceeCCEEEEEEecCch
Q psy6490         310 IHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       310 l~~~~i~g~~i~v~~a~~k  328 (398)
                      ||+..|+|+.|+|.++.++
T Consensus       266 mNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             hCCCeeCCeEEEEEecCCC
Confidence            9999999999999998865

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148|consensus

Probab=100.00  E-value=3.2e-33  Score=239.20  Aligned_cols=166  Identities=28%  Similarity=0.513  Sum_probs=151.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ....|||+.|..+++.++|++.|.+||+|.+++|++|..|+++|||+||.|.+.++|++||. |++..|++|.|+-.|+.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            46789999999999999999999999999999999999999999999999999999999998 99999999999999998


Q ss_pred             CCCCCc-------------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HH
Q psy6490         239 PKNRPK-------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VV  304 (398)
Q Consensus       239 ~~~~~~-------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa  304 (398)
                      .+....             ....+++|||+||...+||++|++.|+.||.|.+|+|.+|      +||+||+|++.| +|
T Consensus       141 RKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAa  214 (321)
T KOG0148|consen  141 RKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAA  214 (321)
T ss_pred             cCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHH
Confidence            775322             2335789999999999999999999999999999999999      789999999965 56


Q ss_pred             HHHHHHCCceeCCEEEEEEecCchHHH
Q psy6490         305 DHICEIHFHMIKNKKVECKKAQPKEAV  331 (398)
Q Consensus       305 ~a~~~l~~~~i~g~~i~v~~a~~k~~~  331 (398)
                      +||++||+..|.|..++|.|.+.....
T Consensus       215 hAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  215 HAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             HHHHHhcCceeCceEEEEeccccCCCC
Confidence            788899999999999999998765443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=7.8e-33  Score=264.91  Aligned_cols=215  Identities=25%  Similarity=0.348  Sum_probs=177.6

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      ..|++|+.+.+...+..++..+++....+..+.+.....        .......++|||+|||.++++++|+++|+.||.
T Consensus        44 s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~--------~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~  115 (352)
T TIGR01661        44 SLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP--------SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQ  115 (352)
T ss_pred             cceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc--------cccccccceEEECCccccCCHHHHHHHHhccCC
Confidence            457899999999999999999998877776666654321        112235678999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCc--ccCCCCCCCCCCC---------------------
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGK--KIDPKHATPKNRP---------------------  243 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~--~l~v~~~~~~~~~---------------------  243 (398)
                      |..++++.+..++.++|||||+|.+.++|++|++ +++..+.|+  .|.+.++......                     
T Consensus       116 i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (352)
T TIGR01661       116 IITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVP  195 (352)
T ss_pred             EEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCC
Confidence            9999999998889999999999999999999997 888888774  4555544321100                     


Q ss_pred             --------------------------------------------------------------------ccCccccceeec
Q psy6490         244 --------------------------------------------------------------------KIGNRTKKIFVG  255 (398)
Q Consensus       244 --------------------------------------------------------------------~~~~~~~~l~V~  255 (398)
                                                                                          .......+|||+
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~  275 (352)
T TIGR01661       196 LSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVY  275 (352)
T ss_pred             ccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEe
Confidence                                                                                001112359999


Q ss_pred             CCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEEecCchHH
Q psy6490         256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEA  330 (398)
Q Consensus       256 nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~~a~~k~~  330 (398)
                      |||+++++++|+++|++||.|++|+|++|..++.+||||||+|++.++|.+ +..|||..|+||.|+|.|...|..
T Consensus       276 NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       276 NLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             CCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            999999999999999999999999999999999999999999999766655 557999999999999999988764

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

>KOG0144|consensus

Probab=99.98  E-value=4.1e-32  Score=246.17  Aligned_cols=177  Identities=26%  Similarity=0.440  Sum_probs=150.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C-CCcccCCc--
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V-PIHTLDGK--  230 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~-~~~~~~g~--  230 (398)
                      +..+.+.-++|||-||..++|+||+++|++||.|.+|.|++|+.++.++|||||.|.+.++|.+|+. + |.++|-|-  
T Consensus        28 d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~  107 (510)
T KOG0144|consen   28 DNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHH  107 (510)
T ss_pred             CCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCc
Confidence            3445678899999999999999999999999999999999999999999999999999999999998 4 55567665  


Q ss_pred             ccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HH
Q psy6490         231 KIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CE  309 (398)
Q Consensus       231 ~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~  309 (398)
                      .|.|++++.+.+  .....++|||+-|+..+||.||+++|++||.|++|.|++| ..+.+||||||.|++.|.|.++ ..
T Consensus       108 pvqvk~Ad~E~e--r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika  184 (510)
T KOG0144|consen  108 PVQVKYADGERE--RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKA  184 (510)
T ss_pred             ceeecccchhhh--ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHh
Confidence            455666654433  2345788999999999999999999999999999999999 5799999999999998877655 46


Q ss_pred             HCCce-eCC--EEEEEEecCchHHHhhh
Q psy6490         310 IHFHM-IKN--KKVECKKAQPKEAVQAN  334 (398)
Q Consensus       310 l~~~~-i~g--~~i~v~~a~~k~~~~~~  334 (398)
                      |||.. +.|  ..|.|+||+++.++..+
T Consensus       185 ~ng~~tmeGcs~PLVVkFADtqkdk~~~  212 (510)
T KOG0144|consen  185 LNGTQTMEGCSQPLVVKFADTQKDKDGK  212 (510)
T ss_pred             hccceeeccCCCceEEEecccCCCchHH
Confidence            98864 555  47999999987766543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.98  E-value=2.8e-31  Score=254.17  Aligned_cols=167  Identities=23%  Similarity=0.454  Sum_probs=151.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +..+|||+|||.++++++|+++|+.||+|.+|+|++|+.+|+++|||||+|.+.++|++||+ +++..+.|++|.|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            56899999999999999999999999999999999999999999999999999999999997 89999999999999886


Q ss_pred             CCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC
Q psy6490         239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN  317 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g  317 (398)
                      +...   ....++|||+|||.++++++|+++|+.||.|..++++.+..++.++|||||+|++.++|+.++ +|||..+.|
T Consensus        82 ~~~~---~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g  158 (352)
T TIGR01661        82 PSSD---SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSG  158 (352)
T ss_pred             cccc---ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            5443   234568999999999999999999999999999999999888999999999999987776665 799999887


Q ss_pred             --EEEEEEecCchH
Q psy6490         318 --KKVECKKAQPKE  329 (398)
Q Consensus       318 --~~i~v~~a~~k~  329 (398)
                        +.|+|+|+....
T Consensus       159 ~~~~i~v~~a~~~~  172 (352)
T TIGR01661       159 CTEPITVKFANNPS  172 (352)
T ss_pred             CceeEEEEECCCCC
Confidence              678999987655

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

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

Probab=99.97  E-value=6.7e-31  Score=266.08  Aligned_cols=221  Identities=27%  Similarity=0.404  Sum_probs=182.9

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      ..+++++.+.+..++..++..+++....+....+..........   .......++|||+||+.++|+++|+++|+.||+
T Consensus       128 skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~---~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~  204 (562)
T TIGR01628       128 SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE---AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGE  204 (562)
T ss_pred             cccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccc---cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCC
Confidence            45788999999999999998888776665555543222111111   123345688999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC----CcccCCCCCCCCCCC---------------ccCc
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD----GKKIDPKHATPKNRP---------------KIGN  247 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~----g~~l~v~~~~~~~~~---------------~~~~  247 (398)
                      |.+++++++. +++++|||||+|.+.++|.+|++ +++..+.    |+.|.|.++..+...               ....
T Consensus       205 i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~  283 (562)
T TIGR01628       205 ITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKA  283 (562)
T ss_pred             EEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhccc
Confidence            9999999986 78899999999999999999998 8999998    999988877654332               1123


Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ...+|||+||+.++|+++|+++|++||.|++|+|++| .+|.++|||||+|.+.++|++|+ +|||+.|+|+.|.|.|+.
T Consensus       284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            4567999999999999999999999999999999999 78999999999999977665555 799999999999999999


Q ss_pred             chHHHhh
Q psy6490         327 PKEAVQA  333 (398)
Q Consensus       327 ~k~~~~~  333 (398)
                      .|+.+..
T Consensus       363 ~k~~~~~  369 (562)
T TIGR01628       363 RKEQRRA  369 (562)
T ss_pred             CcHHHHH
Confidence            9887754

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

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

Probab=99.97  E-value=1.6e-30  Score=257.40  Aligned_cols=170  Identities=25%  Similarity=0.425  Sum_probs=152.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +...++|||+|||.++++++|+++|++||.|.+|++++|+.+++++|||||+|.+.++|.+||.+++..+.|+.|.|...
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSS  165 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeec
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             CCCCCC---------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q psy6490         238 TPKNRP---------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC  308 (398)
Q Consensus       238 ~~~~~~---------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~  308 (398)
                      ......         ......++|||+||+..+|+++|+++|+.||.|.+|.|+++..+|.++|||||+|.+.++|..++
T Consensus       166 ~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~  245 (457)
T TIGR01622       166 QAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL  245 (457)
T ss_pred             chhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHH
Confidence            432211         11123578999999999999999999999999999999999999999999999999988776665


Q ss_pred             -HHCCceeCCEEEEEEecCc
Q psy6490         309 -EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       309 -~l~~~~i~g~~i~v~~a~~  327 (398)
                       .|||..|.|+.|+|.|+..
T Consensus       246 ~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       246 EVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HhcCCcEECCEEEEEEEccC
Confidence             6999999999999999764

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

>KOG0145|consensus

Probab=99.97  E-value=2.7e-30  Score=219.87  Aligned_cols=213  Identities=26%  Similarity=0.353  Sum_probs=183.2

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      .-||+|.+..++..+..+++.+|+.+...+.+.+.-.        +++.+......|||.+||..+|..||+.+|+.||.
T Consensus        82 SLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA--------RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGr  153 (360)
T KOG0145|consen   82 SLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA--------RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGR  153 (360)
T ss_pred             ccccceeeecChHHHHHHHhhhcceeeccceEEEEec--------cCChhhhcccceEEecCCccchHHHHHHHHHHhhh
Confidence            4589999999999999999999999988877777432        23344557789999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCc--ccCCCCCCCCCCC---------------------
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGK--KIDPKHATPKNRP---------------------  243 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~--~l~v~~~~~~~~~---------------------  243 (398)
                      |..-+|..|..+|.+||.+||.|...++|++||+ +|+..-.|.  .|.|+.+......                     
T Consensus       154 IItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~  233 (360)
T KOG0145|consen  154 IITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPM  233 (360)
T ss_pred             hhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcc
Confidence            9999999999999999999999999999999998 788776554  4666655442110                     


Q ss_pred             ---------------------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeec
Q psy6490         244 ---------------------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD  284 (398)
Q Consensus       244 ---------------------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~  284 (398)
                                                             .......+|||-||..+.+|.-|+++|..||.|.+|+|++|
T Consensus       234 hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD  313 (360)
T KOG0145|consen  234 HHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRD  313 (360)
T ss_pred             cchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEec
Confidence                                                   00112458999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEeCC-HHHHHHHHHHCCceeCCEEEEEEecCch
Q psy6490         285 QQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       285 ~~~~~~kg~afV~F~~-~eaa~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      ..++++|||+||.+.+ .|+|.++..|||..+++|.|.|.|...|
T Consensus       314 ~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  314 FTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             CCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            9999999999999999 7788999999999999999999997655

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

Probab=99.97  E-value=7.6e-30  Score=258.39  Aligned_cols=217  Identities=21%  Similarity=0.347  Sum_probs=183.8

Q ss_pred             CCCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCC
Q psy6490         107 GDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFG  186 (398)
Q Consensus       107 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G  186 (398)
                      ...+++++.+.+...+..++..++.....+..+.+.+.......      .....++|||+||+.++++++|+++|++||
T Consensus        40 ~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G  113 (562)
T TIGR01628        40 RSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSL------RRSGVGNIFVKNLDKSVDNKALFDTFSKFG  113 (562)
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccccc------cccCCCceEEcCCCccCCHHHHHHHHHhcC
Confidence            34578999999999999999988887777777777664322111      112457899999999999999999999999


Q ss_pred             CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCc--cCccccceeecCCCCCCCH
Q psy6490         187 AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK--IGNRTKKIFVGGVSQDTSA  263 (398)
Q Consensus       187 ~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~--~~~~~~~l~V~nLp~~~te  263 (398)
                      .|++|++..+. +|+++|||||+|.+.++|++|++ +++..++|+.|.+.....+....  .....++|||+||+.++|+
T Consensus       114 ~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te  192 (562)
T TIGR01628       114 NILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNE  192 (562)
T ss_pred             CcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCH
Confidence            99999999886 78899999999999999999997 89999999999887655443332  3445678999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC----CEEEEEEecCchHHH
Q psy6490         264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK----NKKVECKKAQPKEAV  331 (398)
Q Consensus       264 e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~----g~~i~v~~a~~k~~~  331 (398)
                      ++|+++|++||.|.+++++++ .+++++|||||+|++.++|..++ +++|..|+    |+.|.|.++..+.++
T Consensus       193 e~L~~~F~~fG~i~~~~i~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er  264 (562)
T TIGR01628       193 DKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAER  264 (562)
T ss_pred             HHHHHHHHhcCCEEEEEEEEC-CCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhh
Confidence            999999999999999999988 47899999999999977776555 79999999    999999999887766

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

>KOG0145|consensus

Probab=99.96  E-value=2.4e-29  Score=214.13  Aligned_cols=170  Identities=26%  Similarity=0.475  Sum_probs=154.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .++..+.|.|..||..+|+|||+.+|...|+|++|++++|+.+|.+.||+||.|.+++||++|+. +|+..+..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            44577899999999999999999999999999999999999999999999999999999999998 89999999999999


Q ss_pred             CCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHCCce
Q psy6490         236 HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHM  314 (398)
Q Consensus       236 ~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa~a~~~l~~~~  314 (398)
                      ++++...   .-+...|||.+||..+|..||.++|+.||.|...+|+.|.-+|.+||.+||+|+. .|+-++++.|||..
T Consensus       117 yARPSs~---~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  117 YARPSSD---SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             eccCChh---hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            9987765   3345679999999999999999999999999999999999999999999999998 55667777899998


Q ss_pred             eCCE--EEEEEecCchH
Q psy6490         315 IKNK--KVECKKAQPKE  329 (398)
Q Consensus       315 i~g~--~i~v~~a~~k~  329 (398)
                      -.|.  .|.|+|+....
T Consensus       194 P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNPS  210 (360)
T ss_pred             CCCCCCCeEEEecCCcc
Confidence            7664  69999997653

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

Probab=99.96  E-value=3e-28  Score=239.43  Aligned_cols=162  Identities=23%  Similarity=0.442  Sum_probs=134.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC-CcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD-GKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~-g~~l~v~~~  237 (398)
                      ..++|||+|||.+++|++|+++|++||.|.+|+|++| .+|+++|||||+|.+.++|++||+ +++..+. |+.|.|..+
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            5689999999999999999999999999999999999 699999999999999999999998 7776664 555543322


Q ss_pred             CCC----------------------------------------CCC----------------------------------
Q psy6490         238 TPK----------------------------------------NRP----------------------------------  243 (398)
Q Consensus       238 ~~~----------------------------------------~~~----------------------------------  243 (398)
                      ...                                        ...                                  
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~  215 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIA  215 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEE
Confidence            110                                        000                                  


Q ss_pred             ------------ccCccccceeecCCCCCCCHHHHHHHHhhc--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-
Q psy6490         244 ------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQF--GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-  308 (398)
Q Consensus       244 ------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~--G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-  308 (398)
                                  ......++|||+||++++|+|+|+++|++|  |.|++|+++        ++||||+|++.++|++++ 
T Consensus       216 VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~  287 (578)
T TIGR01648       216 VDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMD  287 (578)
T ss_pred             EEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHH
Confidence                        000123579999999999999999999999  999999876        359999999987776665 


Q ss_pred             HHCCceeCCEEEEEEecCchHH
Q psy6490         309 EIHFHMIKNKKVECKKAQPKEA  330 (398)
Q Consensus       309 ~l~~~~i~g~~i~v~~a~~k~~  330 (398)
                      +||+..|+|+.|+|+|+++++.
T Consensus       288 ~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       288 ELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HhCCCEECCEEEEEEEccCCCc
Confidence            6999999999999999988654

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.

>KOG0117|consensus

Probab=99.96  E-value=4.8e-29  Score=227.35  Aligned_cols=168  Identities=24%  Similarity=0.454  Sum_probs=141.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc-CCcccCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL-DGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~-~g~~l~v~~  236 (398)
                      ...+.||||.||.++.|++|..+|++.|+|-+++|+.|+.+|.+||||||.|.+.++|++|++ +|+.+| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            467999999999999999999999999999999999999999999999999999999999998 777765 566665544


Q ss_pred             CCCCCCC-------------------------------------------------------------------------
Q psy6490         237 ATPKNRP-------------------------------------------------------------------------  243 (398)
Q Consensus       237 ~~~~~~~-------------------------------------------------------------------------  243 (398)
                      +..+.+.                                                                         
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            3321110                                                                         


Q ss_pred             -------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHH
Q psy6490         244 -------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICE  309 (398)
Q Consensus       244 -------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~  309 (398)
                                   .....-+.|||+||+.++|||.|+++|+.||.|++|+.++|        ||||.|.+.+ +.+|+.+
T Consensus       241 tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~  312 (506)
T KOG0117|consen  241 TVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKE  312 (506)
T ss_pred             eeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHH
Confidence                         00012236999999999999999999999999999999877        9999999955 5566778


Q ss_pred             HCCceeCCEEEEEEecCchHHHhhh
Q psy6490         310 IHFHMIKNKKVECKKAQPKEAVQAN  334 (398)
Q Consensus       310 l~~~~i~g~~i~v~~a~~k~~~~~~  334 (398)
                      +||+.|+|..|.|.+|++-.+++..
T Consensus       313 ~ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  313 TNGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             hcCceecCceEEEEecCChhhhccc
Confidence            9999999999999999997766554

>KOG0131|consensus

Probab=99.96  E-value=2.1e-29  Score=203.87  Aligned_cols=170  Identities=27%  Similarity=0.436  Sum_probs=153.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ...+||||||+..++++.|.++|-..|+|+++++.+|+.+...+|||||+|.++|+|+-|++ ++...|.||+|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            67899999999999999999999999999999999999999999999999999999999999 78888999999999887


Q ss_pred             CCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE-TVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~-v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                        ..........+|||+||.++++|..|.+.|+.||.|.+ =.|++|..+|.++||+||.|.+.|++.+++ .|||..+.
T Consensus        88 --~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~  165 (203)
T KOG0131|consen   88 --AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLC  165 (203)
T ss_pred             --cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhc
Confidence              22233445578999999999999999999999998775 368899999999999999999988887776 58999999


Q ss_pred             CEEEEEEecCchHHH
Q psy6490         317 NKKVECKKAQPKEAV  331 (398)
Q Consensus       317 g~~i~v~~a~~k~~~  331 (398)
                      +|.|+|.++..++..
T Consensus       166 nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  166 NRPITVSYAFKKDTK  180 (203)
T ss_pred             CCceEEEEEEecCCC
Confidence            999999999876543

>KOG0124|consensus

Probab=99.95  E-value=7.4e-28  Score=214.07  Aligned_cols=169  Identities=21%  Similarity=0.485  Sum_probs=151.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      --++||||.|.+++.|+.||..|..||.|++|.+..|..|+++|||+||+|+-+|.|..|++ +|+..++||.|+|.+..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            34899999999999999999999999999999999999999999999999999999999999 99999999999998654


Q ss_pred             CCCCC--------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHH
Q psy6490         239 PKNRP--------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICE  309 (398)
Q Consensus       239 ~~~~~--------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~  309 (398)
                      .-..-        ++....++|||..++.+++|+||+..|+.||+|++|.+.++...+..|||+||+|++.. .-+++-.
T Consensus       192 NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            42211        22345678999999999999999999999999999999999988999999999999954 5567778


Q ss_pred             HCCceeCCEEEEEEecCch
Q psy6490         310 IHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       310 l~~~~i~g~~i~v~~a~~k  328 (398)
                      ||-+.++|..|+|..+...
T Consensus       272 MNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             cchhhcccceEecccccCC
Confidence            9999999999999887644

>KOG0127|consensus

Probab=99.95  E-value=4.1e-27  Score=219.36  Aligned_cols=174  Identities=24%  Similarity=0.416  Sum_probs=151.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+..+|.|+|||+.+.+.+|+.+|+.||.|.+|.|.+....+.+ |||||.|.+..+|.+||+ +|+..|+||+|-|.|+
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeee
Confidence            34789999999999999999999999999999999987755555 999999999999999999 8999999999999887


Q ss_pred             CCCCCCc-------------------------------------------------------------------------
Q psy6490         238 TPKNRPK-------------------------------------------------------------------------  244 (398)
Q Consensus       238 ~~~~~~~-------------------------------------------------------------------------  244 (398)
                      ..++.-.                                                                         
T Consensus       194 V~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~  273 (678)
T KOG0127|consen  194 VDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGK  273 (678)
T ss_pred             cccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccccccccccccc
Confidence            6532100                                                                         


Q ss_pred             --------------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy6490         245 --------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI  310 (398)
Q Consensus       245 --------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l  310 (398)
                                    .....++|||+|||+++|||+|.++|++||.|.++.|+.++.|++++|+|||.|.+..++..++++
T Consensus       274 ~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~  353 (678)
T KOG0127|consen  274 KESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEA  353 (678)
T ss_pred             CcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHh
Confidence                          000125799999999999999999999999999999999999999999999999999988888875


Q ss_pred             C------C-ceeCCEEEEEEecCchHHHhh
Q psy6490         311 H------F-HMIKNKKVECKKAQPKEAVQA  333 (398)
Q Consensus       311 ~------~-~~i~g~~i~v~~a~~k~~~~~  333 (398)
                      -      | ..|+||.|+|..+..+.+...
T Consensus       354 Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~d  383 (678)
T KOG0127|consen  354 ASPASEDGSVLLDGRLLKVTLAVTRKEAAD  383 (678)
T ss_pred             cCccCCCceEEEeccEEeeeeccchHHHHH
Confidence            3      4 779999999999988775544

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

Probab=99.95  E-value=4.1e-27  Score=236.28  Aligned_cols=166  Identities=16%  Similarity=0.316  Sum_probs=139.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcC------------CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMF------------GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP  223 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~------------G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~  223 (398)
                      ......++|||||||.++|+++|+++|..|            +.|..+.+.      +.+|||||+|.+.++|..||+++
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~------~~kg~afVeF~~~e~A~~Al~l~  243 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN------KEKNFAFLEFRTVEEATFAMALD  243 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC------CCCCEEEEEeCCHHHHhhhhcCC
Confidence            334477999999999999999999999875            244444443      35899999999999999999999


Q ss_pred             CcccCCcccCCCCCCCCCCC--------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCee
Q psy6490         224 IHTLDGKKIDPKHATPKNRP--------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE  277 (398)
Q Consensus       224 ~~~~~g~~l~v~~~~~~~~~--------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~  277 (398)
                      +..|.|+.|.|.........                          ......++|||+|||..+|+++|+++|+.||.|+
T Consensus       244 g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~  323 (509)
T TIGR01642       244 SIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLK  323 (509)
T ss_pred             CeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCee
Confidence            99999999988754322100                          0122356899999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         278 ETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       278 ~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      .+.|+++..+|.++|||||+|.+.++|..|+ .|||..|+|+.|.|.++..
T Consensus       324 ~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       324 AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            9999999999999999999999988776665 6999999999999999864

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

>KOG0127|consensus

Probab=99.95  E-value=5.6e-27  Score=218.51  Aligned_cols=170  Identities=25%  Similarity=0.459  Sum_probs=149.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      .||||++||++++.++|.++|+.+|.|..+.++.++.++.++||+||.|.-.||+++|++ .....|+|+.|+|..+..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            899999999999999999999999999999999999999999999999999999999998 6788899999999888765


Q ss_pred             CCCcc-----------------------CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEE
Q psy6490         241 NRPKI-----------------------GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT  297 (398)
Q Consensus       241 ~~~~~-----------------------~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~  297 (398)
                      .+...                       .....+|.|+|||+.+.+++|+.+|+.||.|.+|.|.+....+.+ |||||.
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~  164 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQ  164 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEE
Confidence            44321                       112557999999999999999999999999999999977655555 999999


Q ss_pred             eCCH-HHHHHHHHHCCceeCCEEEEEEecCchHHHh
Q psy6490         298 FENE-EVVDHICEIHFHMIKNKKVECKKAQPKEAVQ  332 (398)
Q Consensus       298 F~~~-eaa~a~~~l~~~~i~g~~i~v~~a~~k~~~~  332 (398)
                      |.+. ++.+++..+|+..|+||.|-|.||.+|..-.
T Consensus       165 fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye  200 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYE  200 (678)
T ss_pred             EeeHHHHHHHHHhccCceecCceeEEeeeccccccc
Confidence            9995 5555666799999999999999999876443

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

Probab=99.95  E-value=9.9e-27  Score=230.16  Aligned_cols=159  Identities=18%  Similarity=0.217  Sum_probs=135.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh---CCCcccCCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK---VPIHTLDGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~---~~~~~~~g~~l~v~~  236 (398)
                      ++++|||+|||.++++++|+++|+.||.|.+|+++++      ||||||+|.+.++|++|++   +++..++|+.|.|.+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            3689999999999999999999999999999999864      6899999999999999997   477889999999998


Q ss_pred             CCCCCCCcc---------CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH
Q psy6490         237 ATPKNRPKI---------GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI  307 (398)
Q Consensus       237 ~~~~~~~~~---------~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~  307 (398)
                      +..+.....         .....+|||+||++.+|+++|+++|++||.|.+|.|+++..    +|+|||+|++.++|.+|
T Consensus        75 s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A  150 (481)
T TIGR01649        75 STSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHA  150 (481)
T ss_pred             cCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHH
Confidence            865431111         12234799999999999999999999999999999987642    47999999998777666


Q ss_pred             H-HHCCceeCC--EEEEEEecCch
Q psy6490         308 C-EIHFHMIKN--KKVECKKAQPK  328 (398)
Q Consensus       308 ~-~l~~~~i~g--~~i~v~~a~~k  328 (398)
                      + .|||..|.|  +.|+|.|++.+
T Consensus       151 ~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       151 KAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             HHHhcCCcccCCceEEEEEEecCC
Confidence            5 699999964  58999998763

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=99.94  E-value=3.3e-26  Score=229.69  Aligned_cols=220  Identities=14%  Similarity=0.191  Sum_probs=166.7

Q ss_pred             CCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCC----------C-----------CCCCCCCCCCCcEEEEc
Q psy6490         109 SGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDS----------G-----------RSTPTGDDPTSAKLFVG  167 (398)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~-----------~~~~~~~~~~~~~l~v~  167 (398)
                      .+++|+.+.+...+..++. +++....+..+.+........          .           ...........++|||+
T Consensus       223 kg~afVeF~~~e~A~~Al~-l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~  301 (509)
T TIGR01642       223 KNFAFLEFRTVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIG  301 (509)
T ss_pred             CCEEEEEeCCHHHHhhhhc-CCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEe
Confidence            4688999999999998884 665544443333321111000          0           00011122356899999


Q ss_pred             CCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCc--
Q psy6490         168 GLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK--  244 (398)
Q Consensus       168 nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~--  244 (398)
                      |||..+++++|+++|+.||.|..+.++++..+|.++|||||+|.+.++|..|++ +++..|+|++|.|.++.......  
T Consensus       302 nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~  381 (509)
T TIGR01642       302 NLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATI  381 (509)
T ss_pred             CCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCc
Confidence            999999999999999999999999999999999999999999999999999997 89999999999887764322110  


Q ss_pred             -----------------------cCccccceeecCCCCC--C--------CHHHHHHHHhhcCCeeEEEEeecC---CCC
Q psy6490         245 -----------------------IGNRTKKIFVGGVSQD--T--------SAEEVKAYFSQFGKVEETVMLMDQ---QTK  288 (398)
Q Consensus       245 -----------------------~~~~~~~l~V~nLp~~--~--------tee~L~~~F~~~G~i~~v~i~~~~---~~~  288 (398)
                                             ....+++|+|.||...  +        ..++|+++|++||.|++|+|.++.   .++
T Consensus       382 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~  461 (509)
T TIGR01642       382 DTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNST  461 (509)
T ss_pred             cccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcC
Confidence                                   0124567899999542  1        236899999999999999998753   345


Q ss_pred             CcceEEEEEeCCHHHHHHH-HHHCCceeCCEEEEEEecCchH
Q psy6490         289 RHRGFGFVTFENEEVVDHI-CEIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       289 ~~kg~afV~F~~~eaa~a~-~~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      .++|+|||+|++.++|++| ..|||..|+|+.|.|.|.....
T Consensus       462 ~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~~  503 (509)
T TIGR01642       462 PGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDC  503 (509)
T ss_pred             CCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHHH
Confidence            6789999999997766555 5799999999999999987544

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

>KOG4205|consensus

Probab=99.94  E-value=3.6e-27  Score=214.27  Aligned_cols=175  Identities=54%  Similarity=0.937  Sum_probs=165.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      +.++|||++|+++++++.|++.|..||+|.+|.+++|+.+++++||+||+|.+.+.+.++|....+.|+|+.|+++.+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            77999999999999999999999999999999999999999999999999999999999999888999999999999988


Q ss_pred             CCCCccCc---cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeC
Q psy6490         240 KNRPKIGN---RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIK  316 (398)
Q Consensus       240 ~~~~~~~~---~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~  316 (398)
                      +.......   ..++|||++|+.++++++++++|++||.|.++.++.|..+.+++||+||.|+++++++.++....+.|.
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~  164 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFN  164 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeec
Confidence            77654433   467899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEecCchHHHhhh
Q psy6490         317 NKKVECKKAQPKEAVQAN  334 (398)
Q Consensus       317 g~~i~v~~a~~k~~~~~~  334 (398)
                      |+.|.|+.|.+|+.....
T Consensus       165 gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  165 GKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             CceeeEeeccchhhcccc
Confidence            999999999999987654

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

Probab=99.94  E-value=4.2e-26  Score=225.66  Aligned_cols=163  Identities=19%  Similarity=0.341  Sum_probs=136.4

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         159 PTSAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..+++|||+||+. .+|+++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++ +++..|.|+.|.|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3678999999997 69999999999999999999999874     7999999999999999998 899999999999876


Q ss_pred             CCCCCCC--------------c--------------------cCccccceeecCCCCCCCHHHHHHHHhhcCC--eeEEE
Q psy6490         237 ATPKNRP--------------K--------------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK--VEETV  280 (398)
Q Consensus       237 ~~~~~~~--------------~--------------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~--i~~v~  280 (398)
                      +......              .                    ...++++|||+|||.++|+++|+++|+.||.  |++|+
T Consensus       348 s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik  427 (481)
T TIGR01649       348 SKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFK  427 (481)
T ss_pred             cccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEE
Confidence            5432100              0                    0123568999999999999999999999998  88888


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEE------EEEEecCch
Q psy6490         281 MLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKK------VECKKAQPK  328 (398)
Q Consensus       281 i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~------i~v~~a~~k  328 (398)
                      +..+. + ..+|+|||+|++.++| +|+..||++.|+|+.      |+|.+++++
T Consensus       428 ~~~~~-~-~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       428 FFPKD-N-ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             EecCC-C-CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            76543 2 3589999999996665 555679999999985      999998754

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0109|consensus

Probab=99.94  E-value=2.4e-27  Score=205.18  Aligned_cols=151  Identities=25%  Similarity=0.515  Sum_probs=138.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      ..|||||||.++++.+|+.+|++||+|++|.|+++        ||||..++...++.||. +++.+|+|..|.|+.++.+
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            47999999999999999999999999999999876        99999999999999998 9999999999999998877


Q ss_pred             CCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHCCceeCCEE
Q psy6490         241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKK  319 (398)
Q Consensus       241 ~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa~a~~~l~~~~i~g~~  319 (398)
                      +     ..+.+|+|+||.+.++.+||+..|++||.|.+|.|++|        |+||.|+. +++.+++.+|++.++.|+.
T Consensus        75 s-----k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~  141 (346)
T KOG0109|consen   75 S-----KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKR  141 (346)
T ss_pred             C-----CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccce
Confidence            4     36788999999999999999999999999999999866        99999998 5666888899999999999


Q ss_pred             EEEEecCchHHHhh
Q psy6490         320 VECKKAQPKEAVQA  333 (398)
Q Consensus       320 i~v~~a~~k~~~~~  333 (398)
                      ++|.++.++-....
T Consensus       142 m~vq~stsrlrtap  155 (346)
T KOG0109|consen  142 MHVQLSTSRLRTAP  155 (346)
T ss_pred             eeeeeeccccccCC
Confidence            99999887654443

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

Probab=99.92  E-value=6.5e-24  Score=210.25  Aligned_cols=218  Identities=22%  Similarity=0.294  Sum_probs=163.1

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCC----CCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHh
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSG----RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG  183 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~  183 (398)
                      ..+++|+.+.+...+..++. +++....+..+.+.........    ...........++|||+|||.++++++|+++|+
T Consensus       130 skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~  208 (457)
T TIGR01622       130 SKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFE  208 (457)
T ss_pred             cceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            45788999999998888875 5544443333333221110000    000111122478999999999999999999999


Q ss_pred             cCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCC-------------------
Q psy6490         184 MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRP-------------------  243 (398)
Q Consensus       184 ~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~-------------------  243 (398)
                      .||.|..|.+..+..+|+++|||||+|.+.++|.+|++ +++..+.|+.|.|.++......                   
T Consensus       209 ~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~  288 (457)
T TIGR01622       209 PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKN  288 (457)
T ss_pred             hcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcC
Confidence            99999999999999999999999999999999999997 8999999999998884321000                   


Q ss_pred             --------------------------------------------------------------------ccCccccceeec
Q psy6490         244 --------------------------------------------------------------------KIGNRTKKIFVG  255 (398)
Q Consensus       244 --------------------------------------------------------------------~~~~~~~~l~V~  255 (398)
                                                                                          ......++|+|.
T Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~  368 (457)
T TIGR01622       289 LNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLS  368 (457)
T ss_pred             CCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEe
Confidence                                                                                001234678899


Q ss_pred             CCCCCCC----------HHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEEe
Q psy6490         256 GVSQDTS----------AEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       256 nLp~~~t----------ee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~~  324 (398)
                      ||-...+          .+||++.|++||.|+.|.|..    ..+.|++||+|++.++|.+ +..|||.+|+||.|.|.+
T Consensus       369 n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~----~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~  444 (457)
T TIGR01622       369 NMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDT----KNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAF  444 (457)
T ss_pred             cCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeC----CCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEE
Confidence            9855443          378999999999999998853    3457999999999776655 557999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      ......
T Consensus       445 ~~~~~~  450 (457)
T TIGR01622       445 VVNDVY  450 (457)
T ss_pred             EcHHHH
Confidence            876553

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.

>KOG0123|consensus

Probab=99.92  E-value=2.5e-24  Score=202.93  Aligned_cols=157  Identities=25%  Similarity=0.448  Sum_probs=144.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      ..||||   +++||..|.++|+.+|+|+++++.+|. |  +.|||||.|.++++|++||+ +|...++|+.|++-|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   999999999999999999999999998 6  99999999999999999998 8999999999999998755


Q ss_pred             CCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEE
Q psy6490         241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKK  319 (398)
Q Consensus       241 ~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~  319 (398)
                      ...        |||.||+.+++.++|.++|+.||.|.+|++.+|. +| ++|| ||+|+++++|++++ ++||..+.|+.
T Consensus        76 ~~~--------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kk  144 (369)
T KOG0123|consen   76 PSL--------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKK  144 (369)
T ss_pred             Cce--------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCe
Confidence            543        9999999999999999999999999999999995 45 9999 99999998887766 68999999999


Q ss_pred             EEEEecCchHHHhhhh
Q psy6490         320 VECKKAQPKEAVQANL  335 (398)
Q Consensus       320 i~v~~a~~k~~~~~~~  335 (398)
                      |.|.....++++....
T Consensus       145 i~vg~~~~~~er~~~~  160 (369)
T KOG0123|consen  145 IYVGLFERKEEREAPL  160 (369)
T ss_pred             eEEeeccchhhhcccc
Confidence            9999999988877544

>KOG0148|consensus

Probab=99.91  E-value=6.6e-24  Score=182.17  Aligned_cols=137  Identities=24%  Similarity=0.466  Sum_probs=115.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      +..+||||+||+.++||+-|..||+..|.|.+++|+.|                                  .|.|.++.
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~----------------------------------e~~v~wa~   49 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD----------------------------------ELKVNWAT   49 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehh----------------------------------hhcccccc
Confidence            36799999999999999999999999999999999987                                  12222222


Q ss_pred             CCCC--CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCcee
Q psy6490         239 PKNR--PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMI  315 (398)
Q Consensus       239 ~~~~--~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i  315 (398)
                      ....  .........|||+.|..+++.|+||+.|.+||+|.+++|++|..|+++|||+||.|-+.++|+. |..|||..|
T Consensus        50 ~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl  129 (321)
T KOG0148|consen   50 APGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL  129 (321)
T ss_pred             CcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee
Confidence            2111  1112235569999999999999999999999999999999999999999999999999766655 558999999


Q ss_pred             CCEEEEEEecCchH
Q psy6490         316 KNKKVECKKAQPKE  329 (398)
Q Consensus       316 ~g~~i~v~~a~~k~  329 (398)
                      ++|.|+-.||..|.
T Consensus       130 G~R~IRTNWATRKp  143 (321)
T KOG0148|consen  130 GRRTIRTNWATRKP  143 (321)
T ss_pred             ccceeeccccccCc
Confidence            99999999998876

>KOG0123|consensus

Probab=99.90  E-value=2.2e-23  Score=196.54  Aligned_cols=211  Identities=23%  Similarity=0.382  Sum_probs=181.0

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      .-+++..++.++..+..++..+|.....+....+.|.....             ..|||.||+.+++.++|.++|+.||.
T Consensus        36 slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~-------------~~~~i~nl~~~~~~~~~~d~f~~~g~  102 (369)
T KOG0123|consen   36 SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP-------------SLVFIKNLDESIDNKSLYDTFSEFGN  102 (369)
T ss_pred             ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC-------------ceeeecCCCcccCcHHHHHHHHhhcC
Confidence            77899999999999999999999988888777776654322             22999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCc-----cCccccceeecCCCCCC
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK-----IGNRTKKIFVGGVSQDT  261 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~-----~~~~~~~l~V~nLp~~~  261 (398)
                      |++|++..|+ +| ++|| ||+|+++++|++|++ +|+..++|++|.|.....+....     .......++|.|++.++
T Consensus       103 ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~  179 (369)
T KOG0123|consen  103 ILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDS  179 (369)
T ss_pred             eeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheecccccc
Confidence            9999999997 44 9999 999999999999998 89999999999987766544322     22345679999999999


Q ss_pred             CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEEecCchHHHhhhh
Q psy6490         262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL  335 (398)
Q Consensus       262 tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~~a~~k~~~~~~~  335 (398)
                      ++++|+++|..||.|..+.++.+. .++++||+||.|++.++|+. +..||+..++|..+.|..+..+.++....
T Consensus       180 ~~~~l~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l  253 (369)
T KOG0123|consen  180 TDEELKDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAEL  253 (369)
T ss_pred             chHHHHHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHH
Confidence            999999999999999999999984 66799999999999776655 45799999999999999998866655443

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

Probab=99.90  E-value=2.5e-22  Score=197.97  Aligned_cols=133  Identities=14%  Similarity=0.279  Sum_probs=107.5

Q ss_pred             CCCCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCC---CCCCCCCCCcEEEEcCCCCCCCHHHHHHHH
Q psy6490         106 SGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRS---TPTGDDPTSAKLFVGGLSWQTSSEKLREYF  182 (398)
Q Consensus       106 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f  182 (398)
                      ....|++|..+.+...+..++..+++....+..+.+...........   .........++|||+||+.++++++|+++|
T Consensus       146 gkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lF  225 (612)
T TIGR01645       146 GKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVF  225 (612)
T ss_pred             CCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHH
Confidence            34568999999999999999999888777666666653322111110   011122355899999999999999999999


Q ss_pred             hcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         183 GMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       183 ~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +.||.|+++++.+|+.++++||||||+|.+.++|.+|++ +|+..++|+.|+|.++.
T Consensus       226 s~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       226 EAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             hhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            999999999999999999999999999999999999998 89999999999876543

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.

>KOG0146|consensus

Probab=99.88  E-value=2.6e-23  Score=178.01  Aligned_cols=172  Identities=23%  Similarity=0.447  Sum_probs=144.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcc-cCC--cccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHT-LDG--KKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~-~~g--~~l~v~  235 (398)
                      ++++||||.|...-+|||++.+|..||.|.+|.+.+.. +|.+||++||.|.+..+|..||. +++.. +-|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            67999999999999999999999999999999999886 78899999999999999999997 54432 332  234444


Q ss_pred             CCCCCCCC------------------------------------------------------------------------
Q psy6490         236 HATPKNRP------------------------------------------------------------------------  243 (398)
Q Consensus       236 ~~~~~~~~------------------------------------------------------------------------  243 (398)
                      +++..+++                                                                        
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            44331100                                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q psy6490         244 --------------------------------------------------------------------------------  243 (398)
Q Consensus       244 --------------------------------------------------------------------------------  243 (398)
                                                                                                      
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                                                                                            


Q ss_pred             -----------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC
Q psy6490         244 -----------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN  300 (398)
Q Consensus       244 -----------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~  300 (398)
                                             .+..+.+.|||-.||.+..+.||..+|-.||.|.+.+++.|+.|+.||+|+||.|++
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                                   011145689999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH-HHCCceeCCEEEEEEecCchHHHh
Q psy6490         301 EEVVDHIC-EIHFHMIKNKKVECKKAQPKEAVQ  332 (398)
Q Consensus       301 ~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~~~~  332 (398)
                      ..++.+++ .|||+.|+-++|+|.+.++|+..+
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            87777655 799999999999999999987543

>KOG0110|consensus

Probab=99.88  E-value=1.1e-22  Score=196.07  Aligned_cols=170  Identities=28%  Similarity=0.467  Sum_probs=144.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCC---CCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT---QRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~---~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ++|||.||++++|.++|..+|..+|.|.++.|...+..   -.|.|||||+|.+.++|..|++ ++++.|+|+.|.++.+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            33999999999999999999999999999988765422   2367999999999999999999 7889999999999888


Q ss_pred             CCC------CCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHH
Q psy6490         238 TPK------NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEI  310 (398)
Q Consensus       238 ~~~------~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l  310 (398)
                      ..+      .........++|+|+|||+..+..+|+++|..||.|++|+|.+....+.++|||||+|-+.+.| .|...|
T Consensus       596 ~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al  675 (725)
T KOG0110|consen  596 ENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDAL  675 (725)
T ss_pred             cCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhh
Confidence            721      1122233357899999999999999999999999999999988766677899999999996555 555578


Q ss_pred             CCceeCCEEEEEEecCchHHH
Q psy6490         311 HFHMIKNKKVECKKAQPKEAV  331 (398)
Q Consensus       311 ~~~~i~g~~i~v~~a~~k~~~  331 (398)
                      ..+.|.||+|.+.|+......
T Consensus       676 ~STHlyGRrLVLEwA~~d~~~  696 (725)
T KOG0110|consen  676 GSTHLYGRRLVLEWAKSDNTM  696 (725)
T ss_pred             cccceechhhheehhccchHH
Confidence            899999999999999887653

>KOG0147|consensus

Probab=99.88  E-value=2.3e-23  Score=195.54  Aligned_cols=177  Identities=20%  Similarity=0.431  Sum_probs=154.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      .++.+.++||+--|...++..+|.+||+.+|.|.+|+++.|+.++.++|.+||+|.+.+++-.||.+.+..+.|..|.|.
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQ  253 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEec
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CCCCCCCC-----------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH
Q psy6490         236 HATPKNRP-----------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV  304 (398)
Q Consensus       236 ~~~~~~~~-----------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa  304 (398)
                      ........           ....+..+|||+||++.+++++|+.+|+.||.|+.|.+.+|.++|.+|||+||+|.+.++|
T Consensus       254 ~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~a  333 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDA  333 (549)
T ss_pred             ccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHH
Confidence            65432211           1112233499999999999999999999999999999999999999999999999999888


Q ss_pred             HHHH-HHCCceeCCEEEEEEecCchHHHh
Q psy6490         305 DHIC-EIHFHMIKNKKVECKKAQPKEAVQ  332 (398)
Q Consensus       305 ~a~~-~l~~~~i~g~~i~v~~a~~k~~~~  332 (398)
                      ++++ .|||..|.||.|+|.....+....
T Consensus       334 r~a~e~lngfelAGr~ikV~~v~~r~~~~  362 (549)
T KOG0147|consen  334 RKALEQLNGFELAGRLIKVSVVTERVDTK  362 (549)
T ss_pred             HHHHHHhccceecCceEEEEEeeeecccc
Confidence            8775 699999999999998876554443

>KOG0144|consensus

Probab=99.87  E-value=2.2e-22  Score=183.18  Aligned_cols=169  Identities=28%  Similarity=0.476  Sum_probs=143.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCc-ccCCc--ccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIH-TLDGK--KIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~-~~~g~--~l~v~  235 (398)
                      +.++||||.|+..+||.||+++|++||.|++|.|.+|. .+.+|||+||.|.+.|-|..||+ +|+. ++.|.  .|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            57899999999999999999999999999999999997 78999999999999999999998 6554 36665  56777


Q ss_pred             CCCCCCCCcc----------------------------------------------------------------------
Q psy6490         236 HATPKNRPKI----------------------------------------------------------------------  245 (398)
Q Consensus       236 ~~~~~~~~~~----------------------------------------------------------------------  245 (398)
                      +++.++.+..                                                                      
T Consensus       202 FADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~  281 (510)
T KOG0144|consen  202 FADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALA  281 (510)
T ss_pred             ecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhh
Confidence            7665221100                                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy6490         246 --------------------------------------------------------------------------------  245 (398)
Q Consensus       246 --------------------------------------------------------------------------------  245 (398)
                                                                                                      
T Consensus       282 ~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~a  361 (510)
T KOG0144|consen  282 AAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVA  361 (510)
T ss_pred             hhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCccc
Confidence                                                                                            


Q ss_pred             -----------------------------------------------------------CccccceeecCCCCCCCHHHH
Q psy6490         246 -----------------------------------------------------------GNRTKKIFVGGVSQDTSAEEV  266 (398)
Q Consensus       246 -----------------------------------------------------------~~~~~~l~V~nLp~~~tee~L  266 (398)
                                                                                 ......|||.+||.+.-+.||
T Consensus       362 a~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l  441 (510)
T KOG0144|consen  362 ASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDL  441 (510)
T ss_pred             ccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHH
Confidence                                                                       001225999999999999999


Q ss_pred             HHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHHHCCceeCCEEEEEEecCchH
Q psy6490         267 KAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICEIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       267 ~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      ...|..||.|++.++..|+.|+.+|.|+||.|++.- +-.++..|||..|+.++++|...+.+.
T Consensus       442 ~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  442 IATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             HHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccC
Confidence            999999999999999999999999999999999955 556677899999999999999876653

>KOG4211|consensus

Probab=99.85  E-value=2e-20  Score=173.69  Aligned_cols=173  Identities=20%  Similarity=0.344  Sum_probs=145.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      .....|-+++||+++|++||++||+.| .|.++.+.++  +|+..|-|||+|.++|++++|+|.+...+..|.|+|-.+.
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAG   84 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccC
Confidence            366889999999999999999999999 4888777665  7999999999999999999999999999999999887665


Q ss_pred             CCCCC--------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy6490         239 PKNRP--------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI  310 (398)
Q Consensus       239 ~~~~~--------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l  310 (398)
                      .....        ........|.+++||+.||++||.+||+..-.|....++.....+++.|.|||.|++.|.++.++..
T Consensus        85 ~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen   85 GAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             CccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH
Confidence            43322        2223566899999999999999999999876665534344445788999999999999999999999


Q ss_pred             CCceeCCEEEEEEecCchHHHhhh
Q psy6490         311 HFHMIKNKKVECKKAQPKEAVQAN  334 (398)
Q Consensus       311 ~~~~i~g~~i~v~~a~~k~~~~~~  334 (398)
                      |...|+-|.|.|-.+.-.+.+...
T Consensus       165 hre~iGhRYIEvF~Ss~~e~~~~~  188 (510)
T KOG4211|consen  165 HRENIGHRYIEVFRSSRAEVKRAA  188 (510)
T ss_pred             HHHhhccceEEeehhHHHHHHhhc
Confidence            999999999999998776665543

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

Probab=99.81  E-value=4.1e-19  Score=146.21  Aligned_cols=86  Identities=27%  Similarity=0.546  Sum_probs=78.9

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+||++++||++|+++|++||.|++|+|++|..+++++|||||+|++.++|++|+ +||+..|+|+.|+|+|
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            456778999999999999999999999999999999999999999999999999988887776 5999999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +..+...
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9876554

>KOG0105|consensus

Probab=99.79  E-value=1.6e-18  Score=141.03  Aligned_cols=147  Identities=17%  Similarity=0.335  Sum_probs=121.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++.+.+|.++|.+||.|.+|.+....   ....||||+|++..+|+.||. .++..++|..|+|+...
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            57899999999999999999999999999999987653   246799999999999999998 78899999999998776


Q ss_pred             CCCCC-----------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEE
Q psy6490         239 PKNRP-----------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF  295 (398)
Q Consensus       239 ~~~~~-----------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~af  295 (398)
                      .....                       .......+|.|++||.+-++.||++++.+-|.|....+.+|       |++.
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~Gv  154 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGV  154 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------ccee
Confidence            53211                       11123457999999999999999999999999998888777       3889


Q ss_pred             EEeCCHHHHHH-HHHHCCceeC
Q psy6490         296 VTFENEEVVDH-ICEIHFHMIK  316 (398)
Q Consensus       296 V~F~~~eaa~a-~~~l~~~~i~  316 (398)
                      |+|.+.|+.+- +.+|....+.
T Consensus       155 V~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  155 VEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eeeeehhhHHHHHHhhcccccc
Confidence            99999776654 4567665553

>KOG4206|consensus

Probab=99.76  E-value=1.8e-17  Score=140.31  Aligned_cols=159  Identities=19%  Similarity=0.382  Sum_probs=134.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHH----HHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~----~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      +..||||.||+..+..++|++    +|+.||+|++|...+   +.+.+|-|||.|.+.+.|-.|++ +++.-+.|+.+++
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            455999999999999999988    999999999998876   56789999999999999999998 8999999999999


Q ss_pred             CCCCCCCCC-----------------------------------------------ccCccccceeecCCCCCCCHHHHH
Q psy6490         235 KHATPKNRP-----------------------------------------------KIGNRTKKIFVGGVSQDTSAEEVK  267 (398)
Q Consensus       235 ~~~~~~~~~-----------------------------------------------~~~~~~~~l~V~nLp~~~tee~L~  267 (398)
                      .++..+...                                               ........+|+.|||.+++.+.|.
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~  164 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLS  164 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHH
Confidence            887653211                                               002345679999999999999999


Q ss_pred             HHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC-CEEEEEEecC
Q psy6490         268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK-NKKVECKKAQ  326 (398)
Q Consensus       268 ~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~-g~~i~v~~a~  326 (398)
                      .+|+.|...++|+++...     ++.|||+|.++..+..+. .+.+..|- ...+.|.+++
T Consensus       165 ~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  165 DLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999987653     679999999977776666 57888776 7788887764

>KOG0147|consensus

Probab=99.76  E-value=2.3e-18  Score=162.09  Aligned_cols=163  Identities=25%  Similarity=0.388  Sum_probs=129.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      -..||||||.+++++++|+.+|+.||.|..|.+.+|..||.+||||||+|.+.++|++|++ +|+..|-|+.|.|.....
T Consensus       278 ~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  278 MRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            3449999999999999999999999999999999999999999999999999999999977 999999999987654322


Q ss_pred             CCCCc---------------------------------------------------------------------cC----
Q psy6490         240 KNRPK---------------------------------------------------------------------IG----  246 (398)
Q Consensus       240 ~~~~~---------------------------------------------------------------------~~----  246 (398)
                      +....                                                                     ..    
T Consensus       358 r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p  437 (549)
T KOG0147|consen  358 RVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASP  437 (549)
T ss_pred             ecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcccccc
Confidence            11000                                                                     00    


Q ss_pred             ---ccccceeecCC--CCCCC--------HHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCC
Q psy6490         247 ---NRTKKIFVGGV--SQDTS--------AEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHF  312 (398)
Q Consensus       247 ---~~~~~l~V~nL--p~~~t--------ee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~  312 (398)
                         ..+.|+.++|+  |.+.|        +|||.+.+++||.|..|.|.+.     +-|+.||+|.+.++|.+ +.+|||
T Consensus       438 ~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhg  512 (549)
T KOG0147|consen  438 AFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHG  512 (549)
T ss_pred             ccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhh
Confidence               12345667776  22222        3788999999999998877433     34899999999777655 558999


Q ss_pred             ceeCCEEEEEEecCch
Q psy6490         313 HMIKNKKVECKKAQPK  328 (398)
Q Consensus       313 ~~i~g~~i~v~~a~~k  328 (398)
                      .+|.||.|+..|-...
T Consensus       513 rWF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  513 RWFAGRMITAKYLPLE  528 (549)
T ss_pred             hhhccceeEEEEeehh
Confidence            9999999999986543

>KOG4212|consensus

Probab=99.76  E-value=1.8e-17  Score=151.35  Aligned_cols=164  Identities=20%  Similarity=0.399  Sum_probs=140.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHh-cCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~-~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ..+.+||.|||+++.+.+|+++|. +.|+|+.|.+..|. +|++||+|.|+|+++|.+++|++ ++...++||.|.|+..
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            557799999999999999999996 78899999999997 89999999999999999999998 8999999999988765


Q ss_pred             CCCCCC------------------------------------------cc------------------------------
Q psy6490         238 TPKNRP------------------------------------------KI------------------------------  245 (398)
Q Consensus       238 ~~~~~~------------------------------------------~~------------------------------  245 (398)
                      ......                                          ++                              
T Consensus       122 ~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~  201 (608)
T KOG4212|consen  122 HDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSA  201 (608)
T ss_pred             CchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchh
Confidence            541100                                          00                              


Q ss_pred             ----------CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHCCce
Q psy6490         246 ----------GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHM  314 (398)
Q Consensus       246 ----------~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa~a~~~l~~~~  314 (398)
                                .....++||.||.+.+..+.|++.|.--|.|..|.+-.|+ .|.++|||.++|+. .|+.+++-.+++.-
T Consensus       202 ~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpveavqaIsml~~~g  280 (608)
T KOG4212|consen  202 SFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEAVQAISMLDRQG  280 (608)
T ss_pred             hhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHHHHHHHhhccCC
Confidence                      0012368999999999999999999999999999999996 46999999999988 68888888888877


Q ss_pred             eCCEEEEEEec
Q psy6490         315 IKNKKVECKKA  325 (398)
Q Consensus       315 i~g~~i~v~~a  325 (398)
                      +.+++.+++..
T Consensus       281 ~~~~~~~~Rl~  291 (608)
T KOG4212|consen  281 LFDRRMTVRLD  291 (608)
T ss_pred             Cccccceeecc
Confidence            78888877763

>KOG1548|consensus

Probab=99.73  E-value=1.2e-16  Score=142.25  Aligned_cols=166  Identities=18%  Similarity=0.334  Sum_probs=133.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEE--------EEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD--------VLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG  229 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~--------~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g  229 (398)
                      ..++.|||.|||.++|.+++.++|++||.|..        |++.++. .|+.||-|++.|...|+++.|++ +++..|.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            35677999999999999999999999997753        7888887 59999999999999999999999 78999999


Q ss_pred             cccCCCCCCCCC-----------------------------------CCccCccccceeecCCCC----CCC-------H
Q psy6490         230 KKIDPKHATPKN-----------------------------------RPKIGNRTKKIFVGGVSQ----DTS-------A  263 (398)
Q Consensus       230 ~~l~v~~~~~~~-----------------------------------~~~~~~~~~~l~V~nLp~----~~t-------e  263 (398)
                      +.|+|..+.-..                                   ........++|.|+||=.    ..+       +
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            999987664311                                   011223456899999822    233       4


Q ss_pred             HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchH
Q psy6490         264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       264 e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      ++|++-+++||.|.+|.|.    ...+.|.+-|.|.+.+.|..++ -|+|.+|+||.|.-.....+.
T Consensus       291 edl~eec~K~G~v~~vvv~----d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVY----DRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             HHHHHHHHHhCCcceEEEe----ccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcc
Confidence            6788889999999998874    3456889999999976665555 699999999999998876544

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

Probab=99.72  E-value=3.7e-17  Score=134.61  Aligned_cols=84  Identities=37%  Similarity=0.662  Sum_probs=78.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ..+++|||+||+.++||++|+++|++||.|.+|+++.|+.+++++|||||+|.+.++|++|++ +++..|+|+.|.|+++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            367899999999999999999999999999999999999999999999999999999999997 8999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      ..+..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

>KOG0124|consensus

Probab=99.71  E-value=6.4e-17  Score=144.65  Aligned_cols=219  Identities=15%  Similarity=0.241  Sum_probs=164.4

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCC---CCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhc
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRS---TPTGDDPTSAKLFVGGLSWQTSSEKLREYFGM  184 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~  184 (398)
                      -.+..|..++-++.+.++...+|+.-..+..+.++..++-.....   .-..+...-++|||..+..+++|+||+.+|+.
T Consensus       154 HKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEA  233 (544)
T KOG0124|consen  154 HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEA  233 (544)
T ss_pred             ccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHh
Confidence            345677788899999999999998776666666653332221110   00122346689999999999999999999999


Q ss_pred             CCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCC--------------------
Q psy6490         185 FGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRP--------------------  243 (398)
Q Consensus       185 ~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~--------------------  243 (398)
                      ||+|+.|.+-++...+.+|||||++|.+..+-..|+. +|-..|+|..|+|..+......                    
T Consensus       234 FG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAA  313 (544)
T KOG0124|consen  234 FGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAA  313 (544)
T ss_pred             hcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHH
Confidence            9999999999999889999999999999999999998 7888899998887654330000                    


Q ss_pred             --------------------------------------------------------------------------------
Q psy6490         244 --------------------------------------------------------------------------------  243 (398)
Q Consensus       244 --------------------------------------------------------------------------------  243 (398)
                                                                                                      
T Consensus       314 aTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~pp  393 (544)
T KOG0124|consen  314 ATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPP  393 (544)
T ss_pred             HHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCC
Confidence                                                                                            


Q ss_pred             -----------------------------------------------ccCccccceeecCC--CCCCCH---HHHHHHHh
Q psy6490         244 -----------------------------------------------KIGNRTKKIFVGGV--SQDTSA---EEVKAYFS  271 (398)
Q Consensus       244 -----------------------------------------------~~~~~~~~l~V~nL--p~~~te---e~L~~~F~  271 (398)
                                                                     .+...++.|.++|+  |.+++|   ++|++.|+
T Consensus       394 T~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECg  473 (544)
T KOG0124|consen  394 TLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECG  473 (544)
T ss_pred             chhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHh
Confidence                                                           00013445788888  666654   68999999


Q ss_pred             hcCCeeEEEEeecCCCCCc----ceEEEEEeCCH-HHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         272 QFGKVEETVMLMDQQTKRH----RGFGFVTFENE-EVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       272 ~~G~i~~v~i~~~~~~~~~----kg~afV~F~~~-eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      +||.|.+|.|...+.++..    ----||+|... |.-++...|+|..|+||++..+..+
T Consensus       474 KfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~YD  533 (544)
T KOG0124|consen  474 KFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKVVAEVYD  533 (544)
T ss_pred             cccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCceeehhhhh
Confidence            9999999998877654422    23479999985 5555566799999999999876643

>KOG0149|consensus

Probab=99.69  E-value=3.3e-17  Score=138.97  Aligned_cols=82  Identities=37%  Similarity=0.710  Sum_probs=77.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      +..-++|||+||++++.+|+|+++|++||+|++.+|+.|+.+|+||||+||+|.|.|+|.++++--+-.|+||+..|++|
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA   88 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLA   88 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchh
Confidence            34567899999999999999999999999999999999999999999999999999999999998899999999999987


Q ss_pred             Cc
Q psy6490         326 QP  327 (398)
Q Consensus       326 ~~  327 (398)
                      .-
T Consensus        89 ~l   90 (247)
T KOG0149|consen   89 SL   90 (247)
T ss_pred             hh
Confidence            65

>KOG0149|consensus

Probab=99.67  E-value=1.8e-16  Score=134.47  Aligned_cols=83  Identities=39%  Similarity=0.747  Sum_probs=77.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ..-++||||+|++++..++|+++|++||+|++..|+.|+.+|+|||||||+|+|.|+|.+|++.-.-.|+||+-.+..+.
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLAS   89 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhh
Confidence            36689999999999999999999999999999999999999999999999999999999999988889999999888776


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      -..
T Consensus        90 lg~   92 (247)
T KOG0149|consen   90 LGG   92 (247)
T ss_pred             hcC
Confidence            533

>KOG0125|consensus

Probab=99.67  E-value=2e-16  Score=139.90  Aligned_cols=105  Identities=25%  Similarity=0.463  Sum_probs=86.5

Q ss_pred             CcccCCcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHH
Q psy6490         224 IHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV  303 (398)
Q Consensus       224 ~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~ea  303 (398)
                      +...+|..+....+....   ..+..++|+|+|||+...|-||+.+|++||.|.+|+|+.+.  ..||||+||+|++.++
T Consensus        74 ~~~t~g~~~~~~~st~s~---s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~d  148 (376)
T KOG0125|consen   74 GAPTDGQPIQTQPSTNSS---SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPAD  148 (376)
T ss_pred             CCCCCCCccccCCCCcCC---CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhh
Confidence            334566666555544333   24556789999999999999999999999999999999883  5589999999999988


Q ss_pred             HHHHH-HHCCceeCCEEEEEEecCchHHHhh
Q psy6490         304 VDHIC-EIHFHMIKNKKVECKKAQPKEAVQA  333 (398)
Q Consensus       304 a~a~~-~l~~~~i~g~~i~v~~a~~k~~~~~  333 (398)
                      |+++. +|||..|.||+|+|+.+..+...++
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATarV~n~K  179 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATARVHNKK  179 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchhhccCC
Confidence            88877 7999999999999999998865544

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.67  E-value=3.3e-16  Score=147.20  Aligned_cols=99  Identities=20%  Similarity=0.328  Sum_probs=83.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||+++||++|+++|+.||.|++|+|++|..+++++|||||+|.++++|+.|+ +||+..|.++.|+|.|
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            345788999999999999999999999999999999999999999999999999988777666 7999999999999999


Q ss_pred             cCchHHHhhhhhcCCccccCCCCC
Q psy6490         325 AQPKEAVQANLLVGKRVILGPLGL  348 (398)
Q Consensus       325 a~~k~~~~~~~~~~~~~~~~~~~~  348 (398)
                      +++....    .....++++++..
T Consensus       184 a~p~~~~----~~~~~lfV~nLp~  203 (346)
T TIGR01659       184 ARPGGES----IKDTNLYVTNLPR  203 (346)
T ss_pred             ccccccc----cccceeEEeCCCC
Confidence            8764322    1223456655543

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).

>KOG0122|consensus

Probab=99.66  E-value=3.6e-16  Score=133.13  Aligned_cols=82  Identities=22%  Similarity=0.424  Sum_probs=75.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHHHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....+|.|.||+.+++|+||+++|.+||.|.+|.|.+|++||.+||||||.|++.+ +++|+..|||.-++.-.|+|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            36678999999999999999999999999999999999999999999999999965 55666689999999999999999


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      +++
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            876

>PF00076 RRM_1: RNA recognition motif

Probab=99.65  E-value=8.7e-16  Score=110.80  Aligned_cols=69  Identities=32%  Similarity=0.689  Sum_probs=64.8

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEE
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVE  321 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~  321 (398)
                      |||+|||.++|+++|+++|+.||.|..+.+..+ .++..+|||||+|++.++|+.+++ ++|..++|+.|+
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 788999999999999888887775 999999999986

(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

Probab=99.65  E-value=1.8e-15  Score=146.58  Aligned_cols=164  Identities=22%  Similarity=0.316  Sum_probs=128.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....+.|+|+|||..+..++|.++|..||+|..+.+...      ---++|+|.+..+|..|++ +....+....+.+.
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~------G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle  454 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG------GTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE  454 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcc------cceeeeeecCccchHHHHHHhchhhhccCccccc
Confidence            3446789999999999999999999999999999955421      1249999999999999997 55555655555554


Q ss_pred             CCCCCCCC-----------------------------------------------ccCccccceeecCCCCCCCHHHHHH
Q psy6490         236 HATPKNRP-----------------------------------------------KIGNRTKKIFVGGVSQDTSAEEVKA  268 (398)
Q Consensus       236 ~~~~~~~~-----------------------------------------------~~~~~~~~l~V~nLp~~~tee~L~~  268 (398)
                      |+......                                               ......++|||+||++++|.++|..
T Consensus       455 ~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~  534 (725)
T KOG0110|consen  455 WAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLED  534 (725)
T ss_pred             cChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHH
Confidence            43221000                                               0000122499999999999999999


Q ss_pred             HHhhcCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         269 YFSQFGKVEETVMLMDQQTK---RHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       269 ~F~~~G~i~~v~i~~~~~~~---~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      +|.++|.|.++.|.+.+...   .|.|||||+|.+.++|++++ .|+|+.|+|+.|.|+++.
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            99999999999887664332   36699999999999888877 589999999999999998

>KOG0106|consensus

Probab=99.64  E-value=2.6e-16  Score=134.82  Aligned_cols=153  Identities=20%  Similarity=0.440  Sum_probs=124.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      ..||||+|++.+.+.+|.+||..||.+.++.+.        .||+||+|.+..+|..|+. +++..|.|.++.+.++...
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            469999999999999999999999999999885        4699999999999999997 8888888888877777631


Q ss_pred             C------C-----------CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHH
Q psy6490         241 N------R-----------PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV  303 (398)
Q Consensus       241 ~------~-----------~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~ea  303 (398)
                      .      .           .......+.++|.++...+.+.+|.++|+.+|.+....+        ..+++||+|++.++
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~d  145 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQED  145 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhh
Confidence            0      0           011234567899999999999999999999999965444        25699999999776


Q ss_pred             HHHHH-HHCCceeCCEEEEEEecCchHH
Q psy6490         304 VDHIC-EIHFHMIKNKKVECKKAQPKEA  330 (398)
Q Consensus       304 a~a~~-~l~~~~i~g~~i~v~~a~~k~~  330 (398)
                      ++.++ .+++..+.|+.|++........
T Consensus       146 a~ra~~~l~~~~~~~~~l~~~~~~~d~~  173 (216)
T KOG0106|consen  146 AKRALEKLDGKKLNGRRISVEKNSRDRS  173 (216)
T ss_pred             hhhcchhccchhhcCceeeecccCcchh
Confidence            65555 7999999999999965544433

>KOG0126|consensus

Probab=99.63  E-value=2.6e-17  Score=133.69  Aligned_cols=100  Identities=17%  Similarity=0.395  Sum_probs=85.4

Q ss_pred             ccCCcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHH
Q psy6490         226 TLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV  304 (398)
Q Consensus       226 ~~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa  304 (398)
                      .|+.+.+....+........-..+..|||+|||+++||.||..+|+.||+|.+|.+++|+.||+|+||||+.|++ ....
T Consensus        12 ~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTI   91 (219)
T KOG0126|consen   12 KLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTI   91 (219)
T ss_pred             HhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceE
Confidence            355566665555555555556677889999999999999999999999999999999999999999999999999 4556


Q ss_pred             HHHHHHCCceeCCEEEEEEec
Q psy6490         305 DHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       305 ~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      .|+-.|||..|.||.|+|.-.
T Consensus        92 LAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   92 LAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             EEEeccCCceecceeEEeeec
Confidence            777799999999999999753

>KOG1457|consensus

Probab=99.62  E-value=8.7e-15  Score=122.87  Aligned_cols=155  Identities=15%  Similarity=0.251  Sum_probs=112.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCC-CCCCcccEEEEEEcChHhHHHHHh-CCCcccCC---cc
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG---KK  231 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g---~~  231 (398)
                      +...-+||||.+||.++...||+.+|+.|-..+.+.+.... ...-.+-+|||.|.+..+|..|++ +|+..|+-   ..
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            33468999999999999999999999999877777665432 222356799999999999999998 77777653   33


Q ss_pred             cCCCCCCCCCCCcc------------------------------------------------------------------
Q psy6490         232 IDPKHATPKNRPKI------------------------------------------------------------------  245 (398)
Q Consensus       232 l~v~~~~~~~~~~~------------------------------------------------------------------  245 (398)
                      |.++.++...+..+                                                                  
T Consensus       110 LhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~  189 (284)
T KOG1457|consen  110 LHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSK  189 (284)
T ss_pred             eEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhc
Confidence            44433322110000                                                                  


Q ss_pred             -----------------CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHH
Q psy6490         246 -----------------GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHI  307 (398)
Q Consensus       246 -----------------~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~  307 (398)
                                       ...+.+|||.||..++|||+|+.+|+.|-.....+|...  .|  ...|||+|++.+ +.+++
T Consensus       190 ~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am  265 (284)
T KOG1457|consen  190 APSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAM  265 (284)
T ss_pred             CCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHH
Confidence                             002347999999999999999999999988776665322  33  448999999955 55667


Q ss_pred             HHHCCcee
Q psy6490         308 CEIHFHMI  315 (398)
Q Consensus       308 ~~l~~~~i  315 (398)
                      ..|.|..|
T Consensus       266 ~~lqg~~~  273 (284)
T KOG1457|consen  266 NHLQGNLL  273 (284)
T ss_pred             HHhhccee
Confidence            77887765

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.62  E-value=2e-15  Score=132.72  Aligned_cols=77  Identities=19%  Similarity=0.305  Sum_probs=71.2

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCch
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      .++|||+||++++|+++|+++|+.||.|++|+|++|..   ++|||||+|+++++++.++.|+|..|+|+.|+|.++..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            57899999999999999999999999999999998853   479999999999999999999999999999999998643

>KOG0113|consensus

Probab=99.61  E-value=3.3e-15  Score=130.69  Aligned_cols=90  Identities=19%  Similarity=0.400  Sum_probs=79.6

Q ss_pred             CCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HHHCCceeCCEEE
Q psy6490         242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMIKNKKV  320 (398)
Q Consensus       242 ~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~l~~~~i~g~~i  320 (398)
                      .....++.+||||+-|+++++|.+|++.|+.||.|+.|.|++|+.||+++|||||+|+++-+.++| ...+|..|+|+.|
T Consensus        94 p~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri  173 (335)
T KOG0113|consen   94 PNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRI  173 (335)
T ss_pred             CcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEE
Confidence            334457889999999999999999999999999999999999999999999999999997666555 5789999999999


Q ss_pred             EEEecCchHHH
Q psy6490         321 ECKKAQPKEAV  331 (398)
Q Consensus       321 ~v~~a~~k~~~  331 (398)
                      .|.+-.....+
T Consensus       174 ~VDvERgRTvk  184 (335)
T KOG0113|consen  174 LVDVERGRTVK  184 (335)
T ss_pred             EEEeccccccc
Confidence            99987665543

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

Probab=99.61  E-value=1.5e-15  Score=150.06  Aligned_cols=160  Identities=16%  Similarity=0.187  Sum_probs=122.6

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccc--cccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVV--REAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMF  185 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~  185 (398)
                      ..+.+|+.+.+..++..+...+...  ...+..+.+.+.......   ........++|||+||+.++++++|+++|++|
T Consensus       181 nRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~---d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f  257 (578)
T TIGR01648       181 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEV---DEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF  257 (578)
T ss_pred             cCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccc---cccccccccEEEEeCCCCCCCHHHHHHHHHhc
Confidence            4567889999999998887665432  223344444443322111   11112346899999999999999999999999


Q ss_pred             --CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCc------------------
Q psy6490         186 --GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK------------------  244 (398)
Q Consensus       186 --G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~------------------  244 (398)
                        |.|++|+++        ++||||+|.+.++|++|++ +++..|+|+.|+|.++.+.....                  
T Consensus       258 ~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~  329 (578)
T TIGR01648       258 KPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAA  329 (578)
T ss_pred             CCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcccccccccccCCCccccccc
Confidence              999999875        4599999999999999998 89999999999999887643320                  


Q ss_pred             -------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeE
Q psy6490         245 -------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE  278 (398)
Q Consensus       245 -------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~  278 (398)
                             ......+++++|++++.+++.+.++|..+|.|..
T Consensus       330 ~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~~  370 (578)
T TIGR01648       330 RQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIRG  370 (578)
T ss_pred             ccccCcccCccccccccccccccccccchhhccccCccccC
Confidence                   0124578999999999999999999999998663

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.

>KOG0125|consensus

Probab=99.59  E-value=2.2e-15  Score=133.44  Aligned_cols=82  Identities=29%  Similarity=0.550  Sum_probs=75.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|+|+|||+...|-||+.+|++||+|++|.|+.+.  ..|||||||+|++.+||++|-+ +++..+.||+|+|..+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            366899999999999999999999999999999999984  5589999999999999999987 9999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      ..+..
T Consensus       172 TarV~  176 (376)
T KOG0125|consen  172 TARVH  176 (376)
T ss_pred             chhhc
Confidence            87644

>KOG0129|consensus

Probab=99.58  E-value=5.4e-14  Score=132.16  Aligned_cols=170  Identities=26%  Similarity=0.387  Sum_probs=122.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCC--Cccc---EEEEEEcChHhHHHHHhCCCcccCCc
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ--RSRG---FGFITFAEPETVEKVLKVPIHTLDGK  230 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~--~~~g---~afV~f~~~e~a~~al~~~~~~~~g~  230 (398)
                      ....-++.||||+||.+++|+.|...|..||.+.--+-.+....+  -.+|   |+|+.|+++.++...+......-.+.
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccce
Confidence            334578999999999999999999999999976532222221111  2566   99999999999988775211111111


Q ss_pred             ccCCCCCCCC------------------CCCccCccccceeecCCCCCCCHHHHHHHHh-hcCCeeEEEEeecCCCCCcc
Q psy6490         231 KIDPKHATPK------------------NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFS-QFGKVEETVMLMDQQTKRHR  291 (398)
Q Consensus       231 ~l~v~~~~~~------------------~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~-~~G~i~~v~i~~~~~~~~~k  291 (398)
                      .+.|.....+                  ......+..+||||++||.-++.++|..+|+ -||.|..+-|-+|++-+..|
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCC
Confidence            1211111111                  1223456788999999999999999999999 59999999999999999999


Q ss_pred             eEEEEEeCCHHHHHHHHHHCCceeC----CEEEEEEec
Q psy6490         292 GFGFVTFENEEVVDHICEIHFHMIK----NKKVECKKA  325 (398)
Q Consensus       292 g~afV~F~~~eaa~a~~~l~~~~i~----g~~i~v~~a  325 (398)
                      |-|-|.|.+..+..+|++..-..|+    .|+|+|+-.
T Consensus       414 GaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPY  451 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPY  451 (520)
T ss_pred             CcceeeecccHHHHHHHhhheEEEeccccceeeeecce
Confidence            9999999999988888775444433    346666543

>KOG0121|consensus

Probab=99.58  E-value=3.8e-15  Score=114.22  Aligned_cols=81  Identities=20%  Similarity=0.332  Sum_probs=73.6

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      .+++|||+||++.++||.|.++|+++|+|++|++-.|+.+...-|||||+|.+.++|+.++ -++|+.++++.|+|.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            5789999999999999999999999999999999999999999999999999977776555 699999999999999965


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      .=
T Consensus       115 GF  116 (153)
T KOG0121|consen  115 GF  116 (153)
T ss_pred             cc
Confidence            53

>PF00076 RRM_1: RNA recognition motif

Probab=99.57  E-value=5.6e-15  Score=106.53  Aligned_cols=69  Identities=32%  Similarity=0.717  Sum_probs=65.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       164 l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      |||+|||.++|+++|+++|+.||.|..+++..+ .++..+|||||+|.+.++|++|++ +++..++|++|+
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 588899999999999999999999 899999998873

(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 ....

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

Probab=99.57  E-value=1.5e-14  Score=133.35  Aligned_cols=126  Identities=29%  Similarity=0.569  Sum_probs=108.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC-
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT-  238 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~-  238 (398)
                      .++|||+||+.++++++|+++|..||.|..+.+..|+.++.++|||||+|.+.+++..|++ +++..|.|++|.|.+.. 
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            6999999999999999999999999999999999999899999999999999999999998 78899999999999854 


Q ss_pred             ---CCCCCc-----------------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCC
Q psy6490         239 ---PKNRPK-----------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ  286 (398)
Q Consensus       239 ---~~~~~~-----------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~  286 (398)
                         .+....                 .......+++.+++..++++++...|..+|.+....+.....
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence               211111                 122355789999999999999999999999997776655543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.57  E-value=1.4e-14  Score=104.50  Aligned_cols=69  Identities=28%  Similarity=0.616  Sum_probs=61.5

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEE
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVE  321 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~  321 (398)
                      |||+|||+++++++|+++|+.||.|..+.+..++. +.++|+|||+|.+.++|+.+++ +++..|+|+.|+
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 8999999999999888888775 566999999985

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 ....

>KOG1190|consensus

Probab=99.56  E-value=4e-14  Score=128.84  Aligned_cols=158  Identities=18%  Similarity=0.351  Sum_probs=130.4

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         161 SAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       161 ~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +..|.|.||.. .+|.+.|..+|.-||.|.+|+|..++     +--|+|.|.+...|..|++ +++..+.|++|+|..++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            68899999965 58999999999999999999999986     4579999999999999998 89999999999988776


Q ss_pred             CCCCC--------------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCC
Q psy6490         239 PKNRP--------------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ  286 (398)
Q Consensus       239 ~~~~~--------------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~  286 (398)
                      .....                                ....++.+|.+.|+|.+++||||+.+|..-|...+......  
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~--  449 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ--  449 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC--
Confidence            53210                                01124558999999999999999999999887765544332  


Q ss_pred             CCCcceEEEEEeCC-HHHHHHHHHHCCceeCCE-EEEEEecCc
Q psy6490         287 TKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNK-KVECKKAQP  327 (398)
Q Consensus       287 ~~~~kg~afV~F~~-~eaa~a~~~l~~~~i~g~-~i~v~~a~~  327 (398)
                        +.+-+|++.+++ +|+..+++.+|.+.+++. .++|+|++.
T Consensus       450 --kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  450 --KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             --CCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence              235599999999 667788889999999876 899999864

>KOG0122|consensus

Probab=99.56  E-value=6.5e-15  Score=125.49  Aligned_cols=81  Identities=26%  Similarity=0.409  Sum_probs=77.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +..+|-|.||+.+++|++|+++|..||.|..+.+.+|+.||.+||||||.|.+.++|.+||+ +++.-++.-.|+|+|++
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            77899999999999999999999999999999999999999999999999999999999998 88888888899999988


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            65

>KOG1365|consensus

Probab=99.55  E-value=2.3e-14  Score=129.23  Aligned_cols=171  Identities=18%  Similarity=0.308  Sum_probs=131.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcC----CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMF----GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~----G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ..-.|.+++||+++++.++.+||..-    |..+.|.+++.. +|+..|-|||.|..+++|..||..+...++-|.|++.
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHH
Confidence            45678899999999999999999621    244556555543 7889999999999999999999888888888877654


Q ss_pred             CCCCC----------------------------CCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeE---EEEeec
Q psy6490         236 HATPK----------------------------NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE---TVMLMD  284 (398)
Q Consensus       236 ~~~~~----------------------------~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~---v~i~~~  284 (398)
                      ++...                            ..........+|.+++||++.+.|||.+||..|-.-.+   |.++.+
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N  318 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN  318 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc
Confidence            43321                            00011223678999999999999999999999875333   444444


Q ss_pred             CCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchHHHh
Q psy6490         285 QQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKEAVQ  332 (398)
Q Consensus       285 ~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~~~~  332 (398)
                       ..|+..|.|||+|.++|+|.++. +.|++.+++|.|+|--+...+...
T Consensus       319 -~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln~  366 (508)
T KOG1365|consen  319 -GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELNE  366 (508)
T ss_pred             -CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHHH
Confidence             57899999999999988887765 678888889999999887766554

>KOG0121|consensus

Probab=99.54  E-value=9.7e-15  Score=111.98  Aligned_cols=79  Identities=24%  Similarity=0.471  Sum_probs=74.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++||||||++.++|+.|.++|++||.|..|.|-.|+.+...-|||||+|.+.++|+.|++ +++..|+.+.|.+.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            78999999999999999999999999999999999999888899999999999999999999 89999999999888764

>KOG0120|consensus

Probab=99.54  E-value=3.8e-14  Score=135.60  Aligned_cols=173  Identities=21%  Similarity=0.344  Sum_probs=135.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .......+||++||..++++.++++.+.||.+...+++.|..+|.++||+|.+|.+......|+. +|+..+++++|.+.
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            34467899999999999999999999999999999999999999999999999999999999998 89999999998877


Q ss_pred             CCCCCCCC---------------------ccCccccceeecCC--CCCC-CH-------HHHHHHHhhcCCeeEEEEeec
Q psy6490         236 HATPKNRP---------------------KIGNRTKKIFVGGV--SQDT-SA-------EEVKAYFSQFGKVEETVMLMD  284 (398)
Q Consensus       236 ~~~~~~~~---------------------~~~~~~~~l~V~nL--p~~~-te-------e~L~~~F~~~G~i~~v~i~~~  284 (398)
                      .+......                     .....+..|.+.|+  +.++ ++       |+|+.-|.+||.|.+|.|.++
T Consensus       365 ~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~  444 (500)
T KOG0120|consen  365 RAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRP  444 (500)
T ss_pred             hhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCC
Confidence            65442211                     11112334444444  1111 11       456677888999999999887


Q ss_pred             CC---CCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchH
Q psy6490         285 QQ---TKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       285 ~~---~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      ..   .....|..||+|.+.++++.|+ +|+|.+|.||.|...|.....
T Consensus       445 ~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDk  493 (500)
T KOG0120|consen  445 YPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDK  493 (500)
T ss_pred             CCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHH
Confidence            22   2335678999999977666555 799999999999999986543

>KOG0126|consensus

Probab=99.54  E-value=9.2e-16  Score=124.74  Aligned_cols=92  Identities=20%  Similarity=0.451  Sum_probs=83.2

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCc
Q psy6490         152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGK  230 (398)
Q Consensus       152 ~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~  230 (398)
                      .++..+-.++.-|||||||+++||.||.-+|++||+|++|.+++|+.||+|+||||+.|++..+...|+. +|+..+.||
T Consensus        26 ~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gR  105 (219)
T KOG0126|consen   26 KSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGR  105 (219)
T ss_pred             cchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecce
Confidence            3455566688999999999999999999999999999999999999999999999999999999999997 999999999


Q ss_pred             ccCCCCCCCCCCC
Q psy6490         231 KIDPKHATPKNRP  243 (398)
Q Consensus       231 ~l~v~~~~~~~~~  243 (398)
                      .|+|........+
T Consensus       106 tirVDHv~~Yk~p  118 (219)
T KOG0126|consen  106 TIRVDHVSNYKKP  118 (219)
T ss_pred             eEEeeecccccCC
Confidence            9999877654443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.54  E-value=2.1e-14  Score=126.33  Aligned_cols=79  Identities=16%  Similarity=0.306  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ..++|||+||++++|+++|+++|+.||.|.+|+|.+|+.   ++|||||+|.+.++|+.||.+++..|.|+.|.|.++..
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccC
Confidence            358999999999999999999999999999999998863   47899999999999999999999999999999998765


Q ss_pred             CC
Q psy6490         240 KN  241 (398)
Q Consensus       240 ~~  241 (398)
                      ..
T Consensus        80 ~~   81 (260)
T PLN03120         80 YQ   81 (260)
T ss_pred             CC
Confidence            44

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.53  E-value=4.6e-14  Score=122.15  Aligned_cols=77  Identities=16%  Similarity=0.217  Sum_probs=70.8

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ...+|||+||++++|+++|+++|+.||.|++|+|++|.   ..+|||||+|++.++++.++.|+|..|.|+.|.|..+..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            35789999999999999999999999999999999884   446899999999999999999999999999999987653

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.52  E-value=3.3e-14  Score=102.59  Aligned_cols=69  Identities=32%  Similarity=0.657  Sum_probs=62.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       164 l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      |||+|||.++++++|+++|+.||.|..+++..++. +.++|+|||+|.+.++|.+|++ .++..++|+.|+
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            79999999999999999999999999999999986 8999999999999999999999 455889998763

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 ....

>KOG4207|consensus

Probab=99.52  E-value=2.2e-14  Score=119.15  Aligned_cols=83  Identities=18%  Similarity=0.381  Sum_probs=74.6

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      +.+...+|.|.||-+.++.++|+.+|++||.|-+|.|.+|..|+.++|||||.|.+..+|+.|+ .|+|..|+|+.|+|.
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            3455678999999999999999999999999999999999999999999999999976665555 699999999999999


Q ss_pred             ecCc
Q psy6490         324 KAQP  327 (398)
Q Consensus       324 ~a~~  327 (398)
                      +|+-
T Consensus        89 ~ary   92 (256)
T KOG4207|consen   89 MARY   92 (256)
T ss_pred             hhhc
Confidence            8754

>KOG0114|consensus

Probab=99.51  E-value=1.4e-13  Score=101.68  Aligned_cols=84  Identities=18%  Similarity=0.353  Sum_probs=72.9

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      .+.++.|||+|||+++|.|+..++|.+||.|..|+|-.++.|   +|.|||.|++..+|+.++ .|+|..+.++.+.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            445778999999999999999999999999999999766544   899999999977776665 6999999999999999


Q ss_pred             cCchHHHh
Q psy6490         325 AQPKEAVQ  332 (398)
Q Consensus       325 a~~k~~~~  332 (398)
                      ..+....+
T Consensus        92 yq~~~~~~   99 (124)
T KOG0114|consen   92 YQPEDAFK   99 (124)
T ss_pred             cCHHHHHH
Confidence            88765544

>KOG0117|consensus

Probab=99.51  E-value=1.1e-13  Score=127.53  Aligned_cols=81  Identities=28%  Similarity=0.465  Sum_probs=73.4

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHHHCCceeC-CEEEEEEe
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICEIHFHMIK-NKKVECKK  324 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~l~~~~i~-g~~i~v~~  324 (398)
                      ...+.|||+.||.++.|+||.-+|++.|+|-++++++|+.+|.+||||||.|.+.+ +++|+.+||+++|. ||.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            56788999999999999999999999999999999999999999999999999954 55677789999985 89999988


Q ss_pred             cCc
Q psy6490         325 AQP  327 (398)
Q Consensus       325 a~~  327 (398)
                      +..
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            754

>KOG0113|consensus

Probab=99.50  E-value=4.8e-14  Score=123.49  Aligned_cols=80  Identities=26%  Similarity=0.512  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ++-+||||+-|+++++|.+|+..|+.||.|+.|.|++|+.||+++|||||+|+++.+...|.+ .++..|+|+.|.|..-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            478999999999999999999999999999999999999999999999999999999999998 7899999999977654


Q ss_pred             C
Q psy6490         238 T  238 (398)
Q Consensus       238 ~  238 (398)
                      .
T Consensus       179 R  179 (335)
T KOG0113|consen  179 R  179 (335)
T ss_pred             c
Confidence            3

>KOG0107|consensus

Probab=99.50  E-value=5.1e-14  Score=114.15  Aligned_cols=77  Identities=19%  Similarity=0.415  Sum_probs=69.1

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+||+..+++.||..+|..||.|.+|+|.+.+     -|||||+|++ .+|.+|+..|+|+.|.|..|+|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            46789999999999999999999999999999998754     7899999999 56667778999999999999999987


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      .+.
T Consensus        84 G~~   86 (195)
T KOG0107|consen   84 GRP   86 (195)
T ss_pred             CCc
Confidence            654

>KOG4212|consensus

Probab=99.50  E-value=4.8e-13  Score=122.74  Aligned_cols=72  Identities=14%  Similarity=0.287  Sum_probs=64.0

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      .++|||+|||+++|+..|++-|..||.|+++.|+   +.|+++|  .|+|.++++|+.++ .|++..++||.|+|.+.
T Consensus       536 a~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  536 ACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            3469999999999999999999999999999884   4688887  89999988887776 58999999999999873

>KOG0130|consensus

Probab=99.48  E-value=5.7e-14  Score=108.69  Aligned_cols=88  Identities=18%  Similarity=0.339  Sum_probs=77.8

Q ss_pred             CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HHHCCceeCCEEEE
Q psy6490         243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMIKNKKVE  321 (398)
Q Consensus       243 ~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~l~~~~i~g~~i~  321 (398)
                      +........|||.++..+.+||+|.+.|..||+|+++.+..|..||..||||+|+|++.+.|.++ -.+||..|.|..|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            34445677899999999999999999999999999999999999999999999999996666555 47999999999999


Q ss_pred             EEecCchHH
Q psy6490         322 CKKAQPKEA  330 (398)
Q Consensus       322 v~~a~~k~~  330 (398)
                      |.||-.+..
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999976543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.47  E-value=1.6e-13  Score=118.88  Aligned_cols=78  Identities=15%  Similarity=0.207  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ...+|||+||++++|+++|++||+.||+|.+|+|++|.   ..++||||+|+++++++.|+.+++..|.++.|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            45899999999999999999999999999999999984   456899999999999999999999999999998887654


Q ss_pred             C
Q psy6490         240 K  240 (398)
Q Consensus       240 ~  240 (398)
                      .
T Consensus        81 y   81 (243)
T PLN03121         81 Y   81 (243)
T ss_pred             c
Confidence            3

>PLN03213 repressor of silencing 3; Provisional

Probab=99.47  E-value=1.8e-13  Score=127.23  Aligned_cols=78  Identities=17%  Similarity=0.376  Sum_probs=68.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCH--HHHHH-HHHHCCceeCCEEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE--EVVDH-ICEIHFHMIKNKKVECK  323 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~--eaa~a-~~~l~~~~i~g~~i~v~  323 (398)
                      ....+|||+||+++++++||+.+|..||.|.+|.|+++  +|  ||||||+|.+.  +++.+ +..|||..++||.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            34578999999999999999999999999999999944  66  99999999975  44544 45799999999999999


Q ss_pred             ecCch
Q psy6490         324 KAQPK  328 (398)
Q Consensus       324 ~a~~k  328 (398)
                      .|++.
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            99884

>KOG0146|consensus

Probab=99.46  E-value=1.1e-12  Score=113.20  Aligned_cols=103  Identities=23%  Similarity=0.392  Sum_probs=83.8

Q ss_pred             CcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-H
Q psy6490         229 GKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I  307 (398)
Q Consensus       229 g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~  307 (398)
                      .|.|.|+.+..+.+.   .+.++|||+-|...-+|||++.+|..||.|++|.+.+. .+|.+||||||+|.+..+|.+ |
T Consensus         2 nrpiqvkpadsesrg---~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~s~~eAqaAI   77 (371)
T KOG0146|consen    2 NRPIQVKPADSESRG---GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG-PDGNSKGCAFVKFSSHAEAQAAI   77 (371)
T ss_pred             CCCccccccccccCC---ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC-CCCCCCCceEEEeccchHHHHHH
Confidence            467778777765553   36788999999999999999999999999999999998 479999999999999655555 5


Q ss_pred             HHHCCcee-C--CEEEEEEecCchHHHhhhh
Q psy6490         308 CEIHFHMI-K--NKKVECKKAQPKEAVQANL  335 (398)
Q Consensus       308 ~~l~~~~i-~--g~~i~v~~a~~k~~~~~~~  335 (398)
                      ..|||..- -  ...|.|+|++...+|.-.+
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~lRR  108 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERTLRR  108 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHHHHH
Confidence            57888653 3  5789999998877765543

>KOG0107|consensus

Probab=99.46  E-value=9.9e-14  Score=112.49  Aligned_cols=78  Identities=24%  Similarity=0.570  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      -.+.||||||+.++++.||+.+|..||.|.+|+|-+++     .|||||+|++..+|+.|+. |++..|.|..|.|+.+.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            46899999999999999999999999999999998874     8999999999999999998 89999999999998876


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      ....
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            6544

>KOG0114|consensus

Probab=99.46  E-value=1.6e-13  Score=101.26  Aligned_cols=105  Identities=18%  Similarity=0.343  Sum_probs=83.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      -+.+.++.|||+|||+++|.++..++|.+||.|..|+|-.++.|   +|.|||.|++..+|++|++ +.+..+.++.+.|
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~v   89 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVV   89 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEE
Confidence            34457899999999999999999999999999999999877654   8999999999999999998 8999999999988


Q ss_pred             CCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcC
Q psy6490         235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG  274 (398)
Q Consensus       235 ~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G  274 (398)
                      .+.........           +...-.+++|..+=++||
T Consensus        90 lyyq~~~~~~~-----------~~~~k~~~~l~~~~~ky~  118 (124)
T KOG0114|consen   90 LYYQPEDAFKL-----------MDSRKAREELSILKEKYG  118 (124)
T ss_pred             EecCHHHHHHH-----------HHhHHhhhHHHHHHHHhc
Confidence            77765433211           122334566666666665

>smart00362 RRM_2 RNA recognition motif

Probab=99.44  E-value=7.5e-13  Score=95.27  Aligned_cols=71  Identities=28%  Similarity=0.577  Sum_probs=63.5

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      +|||+|||..+++++|+++|+.||.|.++.+..+.  +.++|+|||+|.+.++|+.++ .+++..++|+.|+|+
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            58999999999999999999999999999998875  778999999999977776655 689999999999874

>KOG4207|consensus

Probab=99.43  E-value=2.3e-13  Score=113.12  Aligned_cols=83  Identities=34%  Similarity=0.538  Sum_probs=77.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      +.+...+|-|-||-+.++.++|+.+|++||.|.+|.|.+|+.|+.++|||||.|.+..+|+.|++ |++.+|+|+.|.|.
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            34467899999999999999999999999999999999999999999999999999999999998 89999999999887


Q ss_pred             CCCC
Q psy6490         236 HATP  239 (398)
Q Consensus       236 ~~~~  239 (398)
                      .+.-
T Consensus        89 ~ary   92 (256)
T KOG4207|consen   89 MARY   92 (256)
T ss_pred             hhhc
Confidence            6543

>smart00360 RRM RNA recognition motif

Probab=99.43  E-value=9e-13  Score=94.50  Aligned_cols=70  Identities=31%  Similarity=0.619  Sum_probs=63.7

Q ss_pred             ecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       254 V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      |+|||.++++++|+++|+.||.|.++.+..++.++.++|+|||+|.+.++|+.++ .+++..++|+.|+|+
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            6899999999999999999999999999998878999999999999988777666 689999999999874

>KOG0108|consensus

Probab=99.41  E-value=6.6e-13  Score=126.61  Aligned_cols=86  Identities=26%  Similarity=0.474  Sum_probs=77.4

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      +.|||+|||++++||+|.++|+..|.|.+++++.|+++|++|||||++|.+.+.+ +++..|||.++.||+|+|.|+...
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            7899999999999999999999999999999999999999999999999996554 556689999999999999998776


Q ss_pred             HHHhhhh
Q psy6490         329 EAVQANL  335 (398)
Q Consensus       329 ~~~~~~~  335 (398)
                      ..+....
T Consensus        99 ~~~~~~~  105 (435)
T KOG0108|consen   99 KNAERSL  105 (435)
T ss_pred             chhHHHH
Confidence            6655443

>KOG0108|consensus

Probab=99.41  E-value=4.8e-13  Score=127.53  Aligned_cols=81  Identities=27%  Similarity=0.541  Sum_probs=77.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      +.|||||||++++|++|.++|+..|.|.+++++.|+.+|+.+||||++|.+.+++.+|++ +++.+++||+|+|.+....
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            899999999999999999999999999999999999999999999999999999999999 8999999999999998765


Q ss_pred             CC
Q psy6490         241 NR  242 (398)
Q Consensus       241 ~~  242 (398)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG0111|consensus

Probab=99.39  E-value=1.7e-13  Score=114.78  Aligned_cols=85  Identities=26%  Similarity=0.601  Sum_probs=76.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHHHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||++|-.+++|.-|...|-+||.|++|.+..|.++.+.|||+||+|+-.| ++.|+-.||+.+|.||.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            345789999999999999999999999999999999999999999999999999855 5555568999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +++..-
T Consensus        87 AkP~ki   92 (298)
T KOG0111|consen   87 AKPEKI   92 (298)
T ss_pred             cCCccc
Confidence            988543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=8.2e-13  Score=122.98  Aligned_cols=77  Identities=22%  Similarity=0.408  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcCh--HhHHHHHh-CCCcccCCcccCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP--ETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~--e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ....+||||||++++++++|+.+|..||.|.+|.|+++  +|  ||||||+|.+.  .++.+||+ +++..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            36689999999999999999999999999999999955  56  99999999987  67999998 99999999999998


Q ss_pred             CCCC
Q psy6490         236 HATP  239 (398)
Q Consensus       236 ~~~~  239 (398)
                      .+++
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            8766

>KOG0120|consensus

Probab=99.38  E-value=1.4e-12  Score=125.06  Aligned_cols=169  Identities=19%  Similarity=0.403  Sum_probs=138.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcC-----------C-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMF-----------G-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI  224 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~-----------G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~  224 (398)
                      .....+.+||++++..++++.+..+|..-           | .+..+.+...      +.|+|++|.+.++|..++.+++
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~------~nfa~ie~~s~~~at~~~~~~~  244 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLE------KNFAFIEFRSISEATEAMALDG  244 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeeccc------ccceeEEecCCCchhhhhcccc
Confidence            34467899999999999999999999643           3 3666666544      6799999999999999999999


Q ss_pred             cccCCcccCCCCCCCCC--------------------CCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeec
Q psy6490         225 HTLDGKKIDPKHATPKN--------------------RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD  284 (398)
Q Consensus       225 ~~~~g~~l~v~~~~~~~--------------------~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~  284 (398)
                      ..+.|+.+.+.......                    .........++||++||..++++.++++.+.||.+....++.|
T Consensus       245 ~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d  324 (500)
T KOG0120|consen  245 IIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKD  324 (500)
T ss_pred             hhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecc
Confidence            89999887765433321                    1122334567999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchHHH
Q psy6490         285 QQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKEAV  331 (398)
Q Consensus       285 ~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~~~  331 (398)
                      ..+|.++||||.+|.+......++ .|||..++++.|.|..+-.....
T Consensus       325 ~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~  372 (500)
T KOG0120|consen  325 SATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASN  372 (500)
T ss_pred             cccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchh
Confidence            999999999999999977665554 69999999999999998665433

>KOG0131|consensus

Probab=99.38  E-value=5.9e-13  Score=108.73  Aligned_cols=80  Identities=26%  Similarity=0.459  Sum_probs=73.9

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      +...+|||+||+..++++-|+++|-..|.|.++.|.+|+.+...+|||||+|.++|+|+-++ -||..+|.||.|+|..+
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            45678999999999999999999999999999999999999999999999999988887655 58999999999999998


Q ss_pred             C
Q psy6490         326 Q  326 (398)
Q Consensus       326 ~  326 (398)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>smart00362 RRM_2 RNA recognition motif

Probab=99.38  E-value=1.9e-12  Score=93.11  Aligned_cols=70  Identities=36%  Similarity=0.638  Sum_probs=64.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      +|||+|||.++++++|+++|+.||.|.++++..++  +.++|+|||+|.+.++|++|++ +++..++|++|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999999999886  6789999999999999999998 6778888888765

>KOG1456|consensus

Probab=99.37  E-value=2.2e-11  Score=109.85  Aligned_cols=161  Identities=16%  Similarity=0.177  Sum_probs=127.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhC---CCcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV---PIHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~---~~~~~~g~~l~v  234 (398)
                      ...+-.|.|++|-..++|.+|.+.++.||.|..+.++..      +..+.|+|++.+.|+.++.+   +...+.|..-.+
T Consensus        28 ~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~  101 (494)
T KOG1456|consen   28 PNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALF  101 (494)
T ss_pred             CCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCcccccCchhhc
Confidence            346789999999999999999999999999998887765      44799999999999999973   555678887777


Q ss_pred             CCCCCCCCC----ccCcccccee--ecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q psy6490         235 KHATPKNRP----KIGNRTKKIF--VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC  308 (398)
Q Consensus       235 ~~~~~~~~~----~~~~~~~~l~--V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~  308 (398)
                      .++......    +....++.|.  |-|--+.+|.|-|..++...|.|.+|.|++.  +   ---|.|+|++.++|++++
T Consensus       102 NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--n---gVQAmVEFdsv~~AqrAk  176 (494)
T KOG1456|consen  102 NYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--N---GVQAMVEFDSVEVAQRAK  176 (494)
T ss_pred             ccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--c---ceeeEEeechhHHHHHHH
Confidence            777543322    2222333343  5555678999999999999999999998766  2   247999999999998888


Q ss_pred             -HHCCcee--CCEEEEEEecCchH
Q psy6490         309 -EIHFHMI--KNKKVECKKAQPKE  329 (398)
Q Consensus       309 -~l~~~~i--~g~~i~v~~a~~k~  329 (398)
                       .|||..|  +-.+|+|++|++..
T Consensus       177 ~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  177 AALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             hhcccccccccceeEEEEecCcce
Confidence             5899876  45789999998743

>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=99.36  E-value=8.1e-12  Score=90.32  Aligned_cols=73  Identities=30%  Similarity=0.611  Sum_probs=64.8

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      +|+|+|||..+++++|+++|+.||.|.++.+..+..+ ..+|+|||+|.+.++|..++ .+++..++|+.|.|.+
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            4899999999999999999999999999999988544 77899999999977776655 6899999999999875

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).

>KOG1190|consensus

Probab=99.36  E-value=3e-12  Score=116.78  Aligned_cols=158  Identities=18%  Similarity=0.274  Sum_probs=117.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh---CCCcccCCcccCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK---VPIHTLDGKKIDPK  235 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~---~~~~~~~g~~l~v~  235 (398)
                      ..++.|.+||||.+++|+||.+++..||+|..+.+.+.      +.-+|++|.++++|...+.   .-.-.+.|+.|.+.
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG------knQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq   99 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG------KNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQ   99 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeecc------chhhhhhhcchhhhhheeecccccCccccCcceeeh
Confidence            47899999999999999999999999999999998875      3379999999999987443   12233667777666


Q ss_pred             CCCCCCCCc-------------------------------------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeE
Q psy6490         236 HATPKNRPK-------------------------------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE  278 (398)
Q Consensus       236 ~~~~~~~~~-------------------------------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~  278 (398)
                      ++..+....                                     ....--+++|.|+-+.++-|-|..+|++||.|.+
T Consensus       100 ~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlK  179 (492)
T KOG1190|consen  100 YSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLK  179 (492)
T ss_pred             hhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEE
Confidence            543321100                                     0011225789999999999999999999999998


Q ss_pred             EEEeecCCCCCcceE-EEEEeCCHHHHHHHH-HHCCceeCC--EEEEEEecCc
Q psy6490         279 TVMLMDQQTKRHRGF-GFVTFENEEVVDHIC-EIHFHMIKN--KKVECKKAQP  327 (398)
Q Consensus       279 v~i~~~~~~~~~kg~-afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v~~a~~  327 (398)
                      |.-+...     .|| |+|.|.+.+.|..++ .|+|..|.+  +.|+|.|++-
T Consensus       180 IiTF~Kn-----n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Skl  227 (492)
T KOG1190|consen  180 IITFTKN-----NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKL  227 (492)
T ss_pred             EEEEecc-----cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhc
Confidence            7654332     334 899999988877766 688888754  4556665543

>KOG0226|consensus

Probab=99.35  E-value=8.1e-13  Score=113.38  Aligned_cols=169  Identities=17%  Similarity=0.322  Sum_probs=129.7

Q ss_pred             CCcEEEEcCCCCCCCHHH-H--HHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEK-L--REYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~-L--~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ....++++++-.++..+- |  ...|+.|-.+...+++++. .+.-++++|+.|.....-.++-. .+++++....|+..
T Consensus        95 ~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a  173 (290)
T KOG0226|consen   95 AVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLA  173 (290)
T ss_pred             ccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeec
Confidence            456677777766666555 3  6678888777777777775 45568899999987776666543 34445555545555


Q ss_pred             CCCCCCCC---ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHHHC
Q psy6490         236 HATPKNRP---KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICEIH  311 (398)
Q Consensus       236 ~~~~~~~~---~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~l~  311 (398)
                      ........   +..+...+||++.|..+++++-|...|.+|-.....++++|+.+|+++||+||.|.+.+ .+.|..+|+
T Consensus       174 ~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~  253 (290)
T KOG0226|consen  174 AGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMN  253 (290)
T ss_pred             cccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhc
Confidence            54444333   34556778999999999999999999999999999999999999999999999999955 556666999


Q ss_pred             CceeCCEEEEEEecCchH
Q psy6490         312 FHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       312 ~~~i~g~~i~v~~a~~k~  329 (398)
                      |++++.|.|+++.+.-++
T Consensus       254 gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  254 GKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             ccccccchhHhhhhhHHh
Confidence            999999999998776655

>KOG0111|consensus

Probab=99.34  E-value=9.9e-13  Score=110.28  Aligned_cols=83  Identities=31%  Similarity=0.515  Sum_probs=79.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++||||+|..+++|.-|...|-.||.|.+|.+..|..+.++|||+||+|...|+|..||. +|..+|.||.|+|..+.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            67999999999999999999999999999999999999999999999999999999999998 99999999999999998


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      +...
T Consensus        89 P~ki   92 (298)
T KOG0111|consen   89 PEKI   92 (298)
T ss_pred             Cccc
Confidence            7554

>smart00360 RRM RNA recognition motif

Probab=99.34  E-value=4.1e-12  Score=90.99  Aligned_cols=69  Identities=36%  Similarity=0.639  Sum_probs=63.7

Q ss_pred             EcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         166 VGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       166 v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      |+|||.++++++|+++|+.||.|.++.+..++.++.++|||||+|.+.++|.+|++ +++..++|+.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            58999999999999999999999999999988888999999999999999999998 6778888888765

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

Probab=99.33  E-value=5e-12  Score=116.46  Aligned_cols=78  Identities=31%  Similarity=0.625  Sum_probs=72.4

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      .++|||+||+.++++++|+++|..||.|..+.+..|+.++.++|||||+|.+.+.+..++ .+++..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            689999999999999999999999999999999999889999999999999987776555 689999999999999965

>KOG1365|consensus

Probab=99.33  E-value=3.6e-12  Score=115.23  Aligned_cols=176  Identities=21%  Similarity=0.282  Sum_probs=137.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      ...++..|..++||+..++.+|..+|.-..-..-.+.+.....|+..|.+.|.|.|.|.-+.|++.+.+.+.++.|.|..
T Consensus        56 ~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYk  135 (508)
T KOG1365|consen   56 SADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYK  135 (508)
T ss_pred             ccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeec
Confidence            34467888899999999999999999755433333444444567778999999999999999999999999999999877


Q ss_pred             CCCCCCCc-------------cCccccceeecCCCCCCCHHHHHHHHhhc----CCeeEEEEeecCCCCCcceEEEEEeC
Q psy6490         237 ATPKNRPK-------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQF----GKVEETVMLMDQQTKRHRGFGFVTFE  299 (398)
Q Consensus       237 ~~~~~~~~-------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~----G~i~~v~i~~~~~~~~~kg~afV~F~  299 (398)
                      +...+-..             .....-.|.+++||+++++.|+.+||..-    |..+.|.+++. .+|+..|-|||.|.
T Consensus       136 a~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa  214 (508)
T KOG1365|consen  136 ATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFA  214 (508)
T ss_pred             cCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEec
Confidence            66543211             11233468899999999999999999732    34555555555 47999999999999


Q ss_pred             CHHHHHHHHHHCCceeCCEEEEEEecCchHHHhh
Q psy6490         300 NEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA  333 (398)
Q Consensus       300 ~~eaa~a~~~l~~~~i~g~~i~v~~a~~k~~~~~  333 (398)
                      .++.|..++..|...|+-|.|++-++...+..+.
T Consensus       215 ~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqv  248 (508)
T KOG1365|consen  215 CEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQV  248 (508)
T ss_pred             CHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHH
Confidence            9999999999999999999999988776665443

>KOG4205|consensus

Probab=99.30  E-value=2e-12  Score=118.25  Aligned_cols=103  Identities=38%  Similarity=0.622  Sum_probs=92.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..++|||++|++++++|.|+++|+.||+|.+|.+++|+.+++++||+||+|.+.+...+++....+.|+||.|.++.+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhh--hcCCccccCCCCCCC
Q psy6490         328 KEAVQANL--LVGKRVILGPLGLRM  350 (398)
Q Consensus       328 k~~~~~~~--~~~~~~~~~~~~~~~  350 (398)
                      +++.....  ...++++++++....
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~  109 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDT  109 (311)
T ss_pred             cccccccccccceeEEEecCcCCCC
Confidence            88766543  246788888765544

>KOG4210|consensus

Probab=99.30  E-value=2.4e-12  Score=117.49  Aligned_cols=173  Identities=18%  Similarity=0.246  Sum_probs=139.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCc-ccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIH-TLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~-~~~g~~l~v~~~~  238 (398)
                      ...++|++++...+.+.++..++..+|.+....+........++|++++.|...+.+..++.+... .+.++.+......
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            578999999999999999999999999888888888777888999999999999999999986664 4555554433332


Q ss_pred             CCC-------CCccCcccccee-ecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy6490         239 PKN-------RPKIGNRTKKIF-VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI  310 (398)
Q Consensus       239 ~~~-------~~~~~~~~~~l~-V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l  310 (398)
                      ...       .........++| |++|++.+++++|+.+|..+|.|..+++..+..++.++|||||.|.+.......+..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            222       112223344555 999999999999999999999999999999999999999999999996555444433


Q ss_pred             CCceeCCEEEEEEecCchHHHh
Q psy6490         311 HFHMIKNKKVECKKAQPKEAVQ  332 (398)
Q Consensus       311 ~~~~i~g~~i~v~~a~~k~~~~  332 (398)
                      ....+.++.+.+.+..+.....
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~  268 (285)
T KOG4210|consen  247 QTRSIGGRPLRLEEDEPRPKSD  268 (285)
T ss_pred             ccCcccCcccccccCCCCcccc
Confidence            8899999999999988775543

>KOG4307|consensus

Probab=99.29  E-value=1.1e-10  Score=113.16  Aligned_cols=175  Identities=10%  Similarity=0.039  Sum_probs=134.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP  234 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v  234 (398)
                      .....+++.+-+.+++++.++.|++++|... .|-.+.|..+...+...|.++|+|....++.+|++.+...+-.|.+.+
T Consensus       305 pqvv~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~  383 (944)
T KOG4307|consen  305 PQVVSDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQT  383 (944)
T ss_pred             CcccchhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceee
Confidence            3444577888899999999999999999643 456666777766666688999999999999999998887777777766


Q ss_pred             CCCCCCCCC------------------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeE
Q psy6490         235 KHATPKNRP------------------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE  278 (398)
Q Consensus       235 ~~~~~~~~~------------------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~  278 (398)
                      .........                                    .......+|||..||..+++.++.++|..--.|++
T Consensus       384 ~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved  463 (944)
T KOG4307|consen  384 GPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVED  463 (944)
T ss_pred             cCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhh
Confidence            544332110                                    11223558999999999999999999998777777


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHH-HHHHHHHCCceeCCEEEEEEecCchHH
Q psy6490         279 TVMLMDQQTKRHRGFGFVTFENEEV-VDHICEIHFHMIKNKKVECKKAQPKEA  330 (398)
Q Consensus       279 v~i~~~~~~~~~kg~afV~F~~~ea-a~a~~~l~~~~i~g~~i~v~~a~~k~~  330 (398)
                      .+.+...-+++-++.|||.|..+++ ..++...+.++++.|.|+|.-...+.+
T Consensus       464 ~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  464 FIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             eeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHHH
Confidence            4333333577889999999999554 466667889999999999988776665

>smart00361 RRM_1 RNA recognition motif

Probab=99.28  E-value=1.9e-11  Score=87.87  Aligned_cols=61  Identities=25%  Similarity=0.448  Sum_probs=52.1

Q ss_pred             HHHHHHHHh----hcCCeeEEE-EeecCCC--CCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEE
Q psy6490         263 AEEVKAYFS----QFGKVEETV-MLMDQQT--KRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECK  323 (398)
Q Consensus       263 ee~L~~~F~----~~G~i~~v~-i~~~~~~--~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~  323 (398)
                      +++|+++|+    +||.|.+|. |+.++.+  +.++|||||+|++.++|.+ +..|||..++||.|++.
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    999999995 7777666  8999999999999777655 55799999999999873

>KOG4211|consensus

Probab=99.28  E-value=4.4e-11  Score=112.01  Aligned_cols=164  Identities=18%  Similarity=0.255  Sum_probs=126.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEE-EEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD-VLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~-~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      .....|-+++||+.||++||.+||+-.-.+.+ +.++.+. .+++.|-|||.|++.|.|++||..+...|+-|.|+|..+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            36789999999999999999999998765554 4455555 567899999999999999999987777777666654322


Q ss_pred             CCCC------------------------CC--------------------------------------------------
Q psy6490         238 TPKN------------------------RP--------------------------------------------------  243 (398)
Q Consensus       238 ~~~~------------------------~~--------------------------------------------------  243 (398)
                      ....                        +.                                                  
T Consensus       180 s~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~  259 (510)
T KOG4211|consen  180 SRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNY  259 (510)
T ss_pred             HHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccccc
Confidence            1100                        00                                                  


Q ss_pred             -c--------------c-CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH
Q psy6490         244 -K--------------I-GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI  307 (398)
Q Consensus       244 -~--------------~-~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~  307 (398)
                       .              . ......++.++||++.++.+|..+|+..-.+ .|.|... .+|+..|.|+|+|.+.++|.++
T Consensus       260 ~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig-~dGr~TGEAdveF~t~edav~A  337 (510)
T KOG4211|consen  260 PVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIG-PDGRATGEADVEFATGEDAVGA  337 (510)
T ss_pred             CCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeC-CCCccCCcceeecccchhhHhh
Confidence             0              0 0011468899999999999999999985544 4666555 5799999999999999999999


Q ss_pred             HHHCCceeCCEEEEEEec
Q psy6490         308 CEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       308 ~~l~~~~i~g~~i~v~~a  325 (398)
                      +..++..+..+.|++-.-
T Consensus       338 mskd~anm~hrYVElFln  355 (510)
T KOG4211|consen  338 MGKDGANMGHRYVELFLN  355 (510)
T ss_pred             hccCCcccCcceeeeccc
Confidence            999999999999887653

>KOG0109|consensus

Probab=99.27  E-value=5.4e-12  Score=110.32  Aligned_cols=86  Identities=20%  Similarity=0.501  Sum_probs=72.2

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      .+|||+|||.++++.+|+.+|++||+|.+|.|+++        ||||..+++.+++.++ +||+.+|.|..|.|+-++.|
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            46999999999999999999999999999999966        9999999988886655 69999999999999999988


Q ss_pred             HHHhhhhhcCCccccCCCCCC
Q psy6490         329 EAVQANLLVGKRVILGPLGLR  349 (398)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~  349 (398)
                      ...      ..++.+|++...
T Consensus        75 sk~------stkl~vgNis~t   89 (346)
T KOG0109|consen   75 SKA------STKLHVGNISPT   89 (346)
T ss_pred             CCC------ccccccCCCCcc
Confidence            322      234555554433

>PF13893 RRM_5: RNA recognition motif

Probab=99.26  E-value=2.9e-11  Score=82.87  Aligned_cols=55  Identities=24%  Similarity=0.466  Sum_probs=47.6

Q ss_pred             HHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       266 L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      |+++|++||.|+++.+..+.     +++|||+|.+.++|+.++ .|||..++|+.|+|.|+
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            68999999999999987663     589999999988887766 59999999999999986

(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 ....

>KOG0130|consensus

Probab=99.26  E-value=1e-11  Score=96.35  Aligned_cols=82  Identities=15%  Similarity=0.321  Sum_probs=77.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ....|||.++..+.+|++|.+.|..||+|+++.+..|+.||-.|||++|+|++.+.|..|+. +|+..|-|..|.|.|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            66889999999999999999999999999999999999999999999999999999999998 89999999999999986


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      .+.
T Consensus       151 v~g  153 (170)
T KOG0130|consen  151 VKG  153 (170)
T ss_pred             ecC
Confidence            554

>KOG0415|consensus

Probab=99.25  E-value=8.6e-12  Score=111.74  Aligned_cols=83  Identities=22%  Similarity=0.423  Sum_probs=75.9

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HHHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~l~~~~i~g~~i~v~~  324 (398)
                      ..+.+.|||..|..-+|+|||.-+|+.||.|.+|.|++|..||.+-.||||+|++.+++++| .+|++..|++|.|+|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            34567899999999999999999999999999999999999999999999999998877665 59999999999999999


Q ss_pred             cCch
Q psy6490         325 AQPK  328 (398)
Q Consensus       325 a~~k  328 (398)
                      +.+-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            7653

>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=99.24  E-value=3.2e-11  Score=87.11  Aligned_cols=72  Identities=39%  Similarity=0.665  Sum_probs=64.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      +|+|+|||.++++++|+++|+.||.|..+.+..+..+ ..+|+|||+|.+.++|..|++ +++..++|+++.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            4899999999999999999999999999999988654 678999999999999999998 67777888887664

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).

>KOG0105|consensus

Probab=99.22  E-value=2.2e-11  Score=99.61  Aligned_cols=80  Identities=19%  Similarity=0.339  Sum_probs=66.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++.+.||.++|.+||.|..|.+...   ...-.||||+|++..+| .|+..-+|..++|..|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            35678999999999999999999999999999987433   22357999999995544 566678999999999999998


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      ..-.
T Consensus        81 rggr   84 (241)
T KOG0105|consen   81 RGGR   84 (241)
T ss_pred             cCCC
Confidence            7653

>KOG4208|consensus

Probab=99.20  E-value=9e-11  Score=98.19  Aligned_cols=92  Identities=25%  Similarity=0.458  Sum_probs=78.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhc-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQF-GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~-G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      ......++|+.+|..+.+.+|..+|..| |.|.++++-|++.||.|||||||+|+++|.|+.+- .||+..|.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3455679999999999999999999998 78888888899999999999999999999887765 599999999999999


Q ss_pred             ecCchHHHhhhhhc
Q psy6490         324 KAQPKEAVQANLLV  337 (398)
Q Consensus       324 ~a~~k~~~~~~~~~  337 (398)
                      +-.+..........
T Consensus       126 vmppe~~v~~~~~k  139 (214)
T KOG4208|consen  126 VMPPEQKVEKNLKK  139 (214)
T ss_pred             EeCchhhhhhhhhh
Confidence            98776444444433

>KOG4454|consensus

Probab=99.19  E-value=5.9e-12  Score=105.73  Aligned_cols=122  Identities=25%  Similarity=0.362  Sum_probs=105.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|+...++|+-|.++|-.-|.|..|.|..++ +++.| ||||.|.++-++.-|++ +|+..+.++.+.++   
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~---   82 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT---   82 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcc---
Confidence            67999999999999999999999999999999998876 55566 99999999999999999 67777777766544   


Q ss_pred             CCCCCccCccccceeecC----CCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC
Q psy6490         239 PKNRPKIGNRTKKIFVGG----VSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN  300 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~n----Lp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~  300 (398)
                                   ++.++    |...+++|.+.+.|+.-|.++.+++.++. +|+++.+.|+.+..
T Consensus        83 -------------~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr  134 (267)
T KOG4454|consen   83 -------------LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQR  134 (267)
T ss_pred             -------------cccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhh
Confidence                         44445    77789999999999999999999999885 48888899998765

>KOG0153|consensus

Probab=99.19  E-value=5.8e-11  Score=106.51  Aligned_cols=80  Identities=24%  Similarity=0.529  Sum_probs=70.3

Q ss_pred             CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH--HCCceeCCEEE
Q psy6490         243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE--IHFHMIKNKKV  320 (398)
Q Consensus       243 ~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~--l~~~~i~g~~i  320 (398)
                      +..+...++|||++|...++|.||+++|.+||+|+.++++..      ++||||+|.+.++|+.+.+  ++...|+|++|
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            344556789999999999999999999999999999999766      6799999999888876653  68889999999


Q ss_pred             EEEecCch
Q psy6490         321 ECKKAQPK  328 (398)
Q Consensus       321 ~v~~a~~k  328 (398)
                      +|.|..++
T Consensus       296 ~i~Wg~~~  303 (377)
T KOG0153|consen  296 KIKWGRPK  303 (377)
T ss_pred             EEEeCCCc
Confidence            99999983

>smart00361 RRM_1 RNA recognition motif

Probab=99.15  E-value=8.3e-11  Score=84.53  Aligned_cols=60  Identities=25%  Similarity=0.469  Sum_probs=53.6

Q ss_pred             HHHHHHHHh----cCCCEEEEE-EeeCCCC--CCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         175 SEKLREYFG----MFGAVTDVL-IMKDPIT--QRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       175 ~~~L~~~f~----~~G~i~~~~-~~~~~~~--~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      +++|+++|+    +||.|.++. +..++.+  +.++||+||+|.+.++|.+|++ +++..++|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578889998    999999995 7777766  8999999999999999999998 8999999998865

>KOG0128|consensus

Probab=99.15  E-value=2.7e-12  Score=127.11  Aligned_cols=148  Identities=22%  Similarity=0.310  Sum_probs=128.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ...++||+||+..+.+.+|...|..+|.+..+++..-+..++.+|+|||+|.+.+++.+|+.+....+.|          
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g----------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG----------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh----------
Confidence            5678999999999999999999999998888877755567889999999999999999999865555555          


Q ss_pred             CCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCE
Q psy6490         240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNK  318 (398)
Q Consensus       240 ~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~  318 (398)
                               ...|+|+|+|+..|.++|+.+|.++|.+.+.+++.. ..|+.+|.|||.|.++..+ ++..+++...++-+
T Consensus       736 ---------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~  805 (881)
T KOG0128|consen  736 ---------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKREN  805 (881)
T ss_pred             ---------hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhc
Confidence                     345999999999999999999999999999997777 5799999999999996555 55667888888888


Q ss_pred             EEEEEecCc
Q psy6490         319 KVECKKAQP  327 (398)
Q Consensus       319 ~i~v~~a~~  327 (398)
                      .+.|..+.+
T Consensus       806 ~~~v~vsnp  814 (881)
T KOG0128|consen  806 NGEVQVSNP  814 (881)
T ss_pred             CccccccCC
Confidence            888888766

>KOG0132|consensus

Probab=99.09  E-value=2.4e-10  Score=112.29  Aligned_cols=80  Identities=15%  Similarity=0.419  Sum_probs=71.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~~a  325 (398)
                      ..++||||++|+..++|.||+.+|+.||.|.+|+++..      +|||||.+.+..+|++ +.+|++..+.++.|+|.|+
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            35789999999999999999999999999999988655      8899999999766655 4589999999999999999


Q ss_pred             CchHHHh
Q psy6490         326 QPKEAVQ  332 (398)
Q Consensus       326 ~~k~~~~  332 (398)
                      ..+..+.
T Consensus       493 ~g~G~ks  499 (894)
T KOG0132|consen  493 VGKGPKS  499 (894)
T ss_pred             ccCCcch
Confidence            9887665

>KOG1456|consensus

Probab=99.07  E-value=4.4e-09  Score=95.25  Aligned_cols=166  Identities=16%  Similarity=0.251  Sum_probs=125.6

Q ss_pred             CCCCCCcEEEEcCCCCC-CCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         156 GDDPTSAKLFVGGLSWQ-TSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~-~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      ....+...+.|.+|... ++-+.|.++|-.||.|+.|++++.+     .|-|.|++.+...+++|+. +++..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            34457899999999765 7779999999999999999999986     6789999999999999998 888888899888


Q ss_pred             CCCCCCCCC----------------------------------CccCccccceeecCCCCCCCHHHHHHHHhhcCC-eeE
Q psy6490         234 PKHATPKNR----------------------------------PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK-VEE  278 (398)
Q Consensus       234 v~~~~~~~~----------------------------------~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~-i~~  278 (398)
                      +..++-...                                  .....++++|..-|.|..+|||.|.++|...+. -.+
T Consensus       357 v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~s  436 (494)
T KOG1456|consen  357 VCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTS  436 (494)
T ss_pred             EeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcce
Confidence            765543110                                  011225667999999999999999999987553 344


Q ss_pred             EEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHCCceeCCE------EEEEEecCch
Q psy6490         279 TVMLMDQQTKRHRGFGFVTFENE-EVVDHICEIHFHMIKNK------KVECKKAQPK  328 (398)
Q Consensus       279 v~i~~~~~~~~~kg~afV~F~~~-eaa~a~~~l~~~~i~g~------~i~v~~a~~k  328 (398)
                      ++|..-+ +.++ .-++++|++. ++.+++..+|...|.+.      .+++.|+.++
T Consensus       437 vkvFp~k-serS-ssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts~  491 (494)
T KOG1456|consen  437 VKVFPLK-SERS-SSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTSK  491 (494)
T ss_pred             EEeeccc-cccc-ccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeecccc
Confidence            5665443 3332 3579999995 56677888888888753      3555555443

>KOG4206|consensus

Probab=99.07  E-value=3.4e-10  Score=96.37  Aligned_cols=84  Identities=23%  Similarity=0.413  Sum_probs=71.9

Q ss_pred             ccccceeecCCCCCCCHHHHHH----HHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKA----YFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVE  321 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~----~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~  321 (398)
                      ..+.||||.||++.+..++|++    +|+.||.|.+|...   .+.+.||-|||.|.+.++| .++..|+|..+.|+.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999999998    99999999988776   3577899999999997666 45557999999999999


Q ss_pred             EEecCchHHHhh
Q psy6490         322 CKKAQPKEAVQA  333 (398)
Q Consensus       322 v~~a~~k~~~~~  333 (398)
                      |.||..+.+...
T Consensus        84 iqyA~s~sdii~   95 (221)
T KOG4206|consen   84 IQYAKSDSDIIA   95 (221)
T ss_pred             eecccCccchhh
Confidence            999988776544

>KOG0132|consensus

Probab=99.07  E-value=1.7e-10  Score=113.35  Aligned_cols=109  Identities=20%  Similarity=0.333  Sum_probs=88.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..-++|||||+|+..++|.||.++|+.||+|.+|.++..      +|+|||.+.+..+|++|+. +....+.++.|++.|
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            345799999999999999999999999999999999875      8899999999999999997 888889999999999


Q ss_pred             CCCCCCCccCcccc--ceeecCCCCCCCHHHHHHHHhh
Q psy6490         237 ATPKNRPKIGNRTK--KIFVGGVSQDTSAEEVKAYFSQ  272 (398)
Q Consensus       237 ~~~~~~~~~~~~~~--~l~V~nLp~~~tee~L~~~F~~  272 (398)
                      +..+..+.+.....  .+=|.-||++.-.+||+.+++.
T Consensus       492 a~g~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~eg  529 (894)
T KOG0132|consen  492 AVGKGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWCEG  529 (894)
T ss_pred             eccCCcchhhhhhhhcccCeeEeehHhcCHHHHHhhhh
Confidence            98776654222221  2356667776555556666654

>KOG0112|consensus

Probab=99.03  E-value=2.9e-10  Score=113.43  Aligned_cols=163  Identities=14%  Similarity=0.255  Sum_probs=126.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      ..+...+++||+|||...+++.+|+..|..+|.|.+|.|..-+. +.-..|+||.|.+...+-.+.- +.+..|..-.+.
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r  444 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHR  444 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccc
Confidence            34455889999999999999999999999999999999977642 3334599999999888777743 444444333333


Q ss_pred             CCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCC
Q psy6490         234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHF  312 (398)
Q Consensus       234 v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~  312 (398)
                      +.....     .....+.+++++|...+....|...|..||.|..|.+-    .|  .-||+|.|++..++.+++ .|.|
T Consensus       445 ~glG~~-----kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~----hg--q~yayi~yes~~~aq~a~~~~rg  513 (975)
T KOG0112|consen  445 IGLGQP-----KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR----HG--QPYAYIQYESPPAAQAATHDMRG  513 (975)
T ss_pred             cccccc-----ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc----cC--CcceeeecccCccchhhHHHHhc
Confidence            333322     34567889999999999999999999999999986653    33  349999999988776665 6899


Q ss_pred             ceeCC--EEEEEEecCchH
Q psy6490         313 HMIKN--KKVECKKAQPKE  329 (398)
Q Consensus       313 ~~i~g--~~i~v~~a~~k~  329 (398)
                      ..|+|  +.+.|.++..-.
T Consensus       514 ap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  514 APLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             CcCCCCCcccccccccCCC
Confidence            98875  679999887644

>PF13893 RRM_5: RNA recognition motif

Probab=99.01  E-value=3.2e-10  Score=77.69  Aligned_cols=55  Identities=31%  Similarity=0.593  Sum_probs=48.8

Q ss_pred             HHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       178 L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      |+++|++||+|.++.+..++     +++|||+|.+.++|++|++ +++..++|++|.|.++
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            68999999999999998764     6899999999999999998 8999999999988753

(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 ....

>KOG4208|consensus

Probab=99.00  E-value=7.3e-10  Score=92.83  Aligned_cols=84  Identities=18%  Similarity=0.336  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcC-CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMF-GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~-G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .......+||+.+|..+.+.+|..+|..+ |.+..+++.|++.||.|||||||+|++++.|+-|-+ ||+..|.++.|.+
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            34467899999999999999999999998 788888998999999999999999999999999988 8888898888877


Q ss_pred             CCCCCC
Q psy6490         235 KHATPK  240 (398)
Q Consensus       235 ~~~~~~  240 (398)
                      ....+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            766544

>KOG0153|consensus

Probab=98.95  E-value=1.5e-09  Score=97.55  Aligned_cols=80  Identities=24%  Similarity=0.503  Sum_probs=72.2

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh--CCCcccCCcc
Q psy6490         154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK--VPIHTLDGKK  231 (398)
Q Consensus       154 ~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~--~~~~~~~g~~  231 (398)
                      ...++....+|||++|-..++|.+|+++|.+||+|+++.+...      +++|||+|.+.++|+.|.+  ++...++|++
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            3345567899999999999999999999999999999999876      6799999999999999987  6778899999


Q ss_pred             cCCCCCCC
Q psy6490         232 IDPKHATP  239 (398)
Q Consensus       232 l~v~~~~~  239 (398)
                      |.|.|...
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999987

>KOG0415|consensus

Probab=98.95  E-value=8.4e-10  Score=99.14  Aligned_cols=82  Identities=27%  Similarity=0.429  Sum_probs=75.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHH-hCCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KVPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al-~~~~~~~~g~~l~v~~  236 (398)
                      .++.+.|||-.|.+-+|+++|.-+|+.||.|.+|.+++|..||.+..||||+|++.+++++|. +|.+..|++++|.|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            447899999999999999999999999999999999999999999999999999999999996 5899999999998876


Q ss_pred             CCC
Q psy6490         237 ATP  239 (398)
Q Consensus       237 ~~~  239 (398)
                      +..
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            543

>KOG0116|consensus

Probab=98.90  E-value=3.4e-09  Score=100.76  Aligned_cols=81  Identities=27%  Similarity=0.438  Sum_probs=70.7

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCch
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      ..+|||+|||.++++++|+++|..||.|+...|......++..+||||+|++.++++.+++.+-..|+++++.|+--++.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecccc
Confidence            34599999999999999999999999999998877654455558999999999999999999999999999999876653


Q ss_pred             H
Q psy6490         329 E  329 (398)
Q Consensus       329 ~  329 (398)
                      -
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            3

>KOG0226|consensus

Probab=98.88  E-value=1.5e-09  Score=93.52  Aligned_cols=87  Identities=20%  Similarity=0.416  Sum_probs=78.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .+.+..+.+||.|.|..+++++.|-..|.+|-.....++++|+.||+++||+||.|.+.+++.+|++ +++.+++.+.|.
T Consensus       184 ~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  184 AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            3456678999999999999999999999999999999999999999999999999999999999998 899999999988


Q ss_pred             CCCCCCCC
Q psy6490         234 PKHATPKN  241 (398)
Q Consensus       234 v~~~~~~~  241 (398)
                      ++.+..+.
T Consensus       264 lRkS~wke  271 (290)
T KOG0226|consen  264 LRKSEWKE  271 (290)
T ss_pred             hhhhhHHh
Confidence            77665444

>KOG4661|consensus

Probab=98.88  E-value=5.6e-09  Score=99.29  Aligned_cols=81  Identities=23%  Similarity=0.459  Sum_probs=75.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      -.++|||.+|...+...+|+.+|++||+|+..+++.+..+-..++|+||++.+.++|.+||+ ++...|.|+.|.|..++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            56899999999999999999999999999999999988777789999999999999999998 89999999999998876


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            53

>KOG4660|consensus

Probab=98.82  E-value=4.9e-09  Score=100.02  Aligned_cols=159  Identities=20%  Similarity=0.203  Sum_probs=111.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ..+...++|+|-|||.+|++++|+.+|+.||+|++|+....     .+|..||+|.|..+|++|++ ++...+.|+.|..
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~  144 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIKR  144 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcC
Confidence            44557899999999999999999999999999999877555     48999999999999999998 8899999998873


Q ss_pred             CCCCCCCCCc-------------------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEE
Q psy6490         235 KHATPKNRPK-------------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF  295 (398)
Q Consensus       235 ~~~~~~~~~~-------------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~af  295 (398)
                      .........-                   .......+|+ .|....+..-++..|.-+|.+.. +.     ++.-+-.-|
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~-----~~~~~hq~~  217 (549)
T KOG4660|consen  145 PGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-MLSPTRSSILLEHISSVDGSSPG-RE-----TPLLNHQRF  217 (549)
T ss_pred             CCcccccchhcccchhhhhccchhhcCCCCCCcCCccee-eeccchhhhhhhcchhccCcccc-cc-----ccchhhhhh
Confidence            2222111100                   0001112333 38888888777778888888775 32     232233567


Q ss_pred             EEeCCHHHH-HHHHHHCCceeCCEEEEEEecCc
Q psy6490         296 VTFENEEVV-DHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       296 V~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ++|.+..++ .+...+ |..+.+....+.++.+
T Consensus       218 ~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  218 VEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             hhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            888774444 333333 7778887777777665

>KOG4307|consensus

Probab=98.79  E-value=1.3e-08  Score=99.11  Aligned_cols=74  Identities=15%  Similarity=0.262  Sum_probs=64.5

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEe
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~  324 (398)
                      .|-+.|+|++++-|||.+||..|-.+-.-++++..+.|+..|.|.|-|++.|.| .|.+.++++.|..|+|+|.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            488999999999999999999998877666667668899999999999996555 55668999999999999875

>KOG0533|consensus

Probab=98.79  E-value=2.2e-08  Score=88.30  Aligned_cols=85  Identities=14%  Similarity=0.281  Sum_probs=72.7

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~~  324 (398)
                      .....+|+|.||++.++++||+++|..||.++.+.+..| ..|.+.|.|-|.|+..++|.+ +..+++..++|+.|++..
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 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            344578999999999999999999999999999988888 589999999999999766655 557999999999999988


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      ..+....
T Consensus       159 i~~~~~~  165 (243)
T KOG0533|consen  159 ISSPSQS  165 (243)
T ss_pred             ecCcccc
Confidence            7654433

>KOG0116|consensus

Probab=98.75  E-value=1.6e-08  Score=96.19  Aligned_cols=82  Identities=21%  Similarity=0.396  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ...+|||+|||.++++++|+++|..||.|+...|......++..+||||+|.+.+++..+|..+...+++++|.|+....
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccc
Confidence            44559999999999999999999999999999887765445555999999999999999999888899999998877655


Q ss_pred             CC
Q psy6490         240 KN  241 (398)
Q Consensus       240 ~~  241 (398)
                      ..
T Consensus       367 ~~  368 (419)
T KOG0116|consen  367 GF  368 (419)
T ss_pred             cc
Confidence            33

>KOG4661|consensus

Probab=98.75  E-value=2.6e-08  Score=94.85  Aligned_cols=81  Identities=25%  Similarity=0.465  Sum_probs=71.7

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ..+.|||.+|...+...||+.+|++||.|+-.+|+.+..+--.++|+||++.+.+.| +.|..||.+.|.||.|.|..++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            456899999999999999999999999999999999877777899999999996555 5555799999999999999987


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            63

>KOG4209|consensus

Probab=98.71  E-value=1.6e-08  Score=89.40  Aligned_cols=83  Identities=17%  Similarity=0.312  Sum_probs=76.6

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....+.+||+|+.+.+|.+++..+|+.||.|..+.|..|+.++.+|||+||+|.+.+.+..++.|++..|.|+.|+|.+.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLK  177 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeee
Confidence            34567899999999999999999999999999999999999999999999999999999888889999999999999987


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      +..
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            654

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

Probab=98.69  E-value=1.4e-07  Score=71.12  Aligned_cols=79  Identities=15%  Similarity=0.226  Sum_probs=67.6

Q ss_pred             cceeecCCCCCCCHHHHHHHHhh--cCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC----CEEEEE
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQ--FGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK----NKKVEC  322 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~--~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~----g~~i~v  322 (398)
                      +||.|+|||...|.++|.+++..  .|...-+.+..|..++.+.|||||.|.+.+++.... .++|+.+.    .+.+.|
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            58999999999999999999986  477788888899889999999999999988877755 68998875    677889


Q ss_pred             EecCch
Q psy6490         323 KKAQPK  328 (398)
Q Consensus       323 ~~a~~k  328 (398)
                      .||+-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            988643

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

>KOG4209|consensus

Probab=98.66  E-value=2.6e-08  Score=88.06  Aligned_cols=85  Identities=20%  Similarity=0.391  Sum_probs=78.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ....+.+.+||+|+.+.+|.+++...|+.||.|..+.+..|+.++.+|||+||+|.+.+.++.++++++..+.|+.+.+.
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVT  175 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceee
Confidence            44557899999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CCCCC
Q psy6490         236 HATPK  240 (398)
Q Consensus       236 ~~~~~  240 (398)
                      +....
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            66543

>KOG1457|consensus

Probab=98.62  E-value=1.6e-07  Score=79.63  Aligned_cols=89  Identities=13%  Similarity=0.251  Sum_probs=70.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC---CEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD-QQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK---NKKVE  321 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~-~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~---g~~i~  321 (398)
                      ..-+||||.+||.++.-.||..+|..|-.-+.+.+... +.....+-+|||.|.+...|.+++ +|||.+|+   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34689999999999999999999999877776665433 222345679999999988777776 69999997   78899


Q ss_pred             EEecCchHHHhhhh
Q psy6490         322 CKKAQPKEAVQANL  335 (398)
Q Consensus       322 v~~a~~k~~~~~~~  335 (398)
                      |++++....+++..
T Consensus       112 iElAKSNtK~kr~k  125 (284)
T KOG1457|consen  112 IELAKSNTKRKRRK  125 (284)
T ss_pred             eeehhcCcccccCC
Confidence            99988776665543

>KOG0533|consensus

Probab=98.60  E-value=1.1e-07  Score=83.96  Aligned_cols=83  Identities=24%  Similarity=0.388  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .+....+|+|.||++.++++||+++|..||.+..+-+-.++ +|.+.|.|-|.|...++|..|++ +++..++|+.+.+.
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            34456899999999999999999999999988888888876 89999999999999999999998 88888999998776


Q ss_pred             CCCCC
Q psy6490         236 HATPK  240 (398)
Q Consensus       236 ~~~~~  240 (398)
                      .....
T Consensus       158 ~i~~~  162 (243)
T KOG0533|consen  158 IISSP  162 (243)
T ss_pred             EecCc
Confidence            65543

>KOG1548|consensus

Probab=98.56  E-value=1.9e-07  Score=84.22  Aligned_cols=78  Identities=17%  Similarity=0.327  Sum_probs=68.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE--------TVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNK  318 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~--------v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~  318 (398)
                      .+..|||.|||.++|.+++.++|++||.|.+        |++.++. .|..||-|++.|-..|++.-|+ -|++..|.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            4567999999999999999999999998763        6788884 5999999999999988887666 5899999999


Q ss_pred             EEEEEecC
Q psy6490         319 KVECKKAQ  326 (398)
Q Consensus       319 ~i~v~~a~  326 (398)
                      .|+|..|+
T Consensus       212 ~~rVerAk  219 (382)
T KOG1548|consen  212 KLRVERAK  219 (382)
T ss_pred             EEEEehhh
Confidence            99999875

>KOG0128|consensus

Probab=98.46  E-value=2.4e-08  Score=99.70  Aligned_cols=158  Identities=17%  Similarity=0.124  Sum_probs=123.1

Q ss_pred             CCcEEEEcCCCCCCCHH-HHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSE-KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~-~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ..+..++.++.....+. ..+..|..+|.|+.|++......-..--+.++.+....+++.+....+..+.++.+.+..+.
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad  649 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLAD  649 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCCC
Confidence            45667788887777665 67888999999999988763222222238899999999999999888888999998888777


Q ss_pred             CCCCCccC-------ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHC
Q psy6490         239 PKNRPKIG-------NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH  311 (398)
Q Consensus       239 ~~~~~~~~-------~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~  311 (398)
                      .+......       ....++||+||+..+.++||...|..+|.++.+.|.....+++.+|+|||.|...+.+.++++++
T Consensus       650 ~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~  729 (881)
T KOG0128|consen  650 AEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR  729 (881)
T ss_pred             chhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhh
Confidence            65532221       23457999999999999999999999999998888767778999999999999987777776654


Q ss_pred             CceeCC
Q psy6490         312 FHMIKN  317 (398)
Q Consensus       312 ~~~i~g  317 (398)
                      ...+.|
T Consensus       730 d~~~~g  735 (881)
T KOG0128|consen  730 DSCFFG  735 (881)
T ss_pred             hhhhhh
Confidence            444333

>KOG4660|consensus

Probab=98.46  E-value=1.6e-07  Score=89.90  Aligned_cols=73  Identities=18%  Similarity=0.295  Sum_probs=62.0

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVE  321 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~  321 (398)
                      ......++|+|-|||.++++++|+.+|+.||+|+.|+.     +-..+|.+||+|-|...| .|+.+|++.+|.|+.|+
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            33557789999999999999999999999999998654     444589999999996555 45568999999999998

>KOG4676|consensus

Probab=98.45  E-value=8.2e-08  Score=87.70  Aligned_cols=159  Identities=12%  Similarity=0.137  Sum_probs=118.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCC---CCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT---QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~---~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ...|.|.||...+|.+.++.||...|+|.+++|..+..+   ......|||.|.+...+..|-.|.+.++-++-|.|...
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            348999999999999999999999999999999764322   22445899999999998888766666666665544332


Q ss_pred             CCCCCC-----------------------------------------------------ccCccccceeecCCCCCCCHH
Q psy6490         238 TPKNRP-----------------------------------------------------KIGNRTKKIFVGGVSQDTSAE  264 (398)
Q Consensus       238 ~~~~~~-----------------------------------------------------~~~~~~~~l~V~nLp~~~tee  264 (398)
                      .....+                                                     ...+-.++++|.+|...+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            221000                                                     001123579999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEE
Q psy6490         265 EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK  323 (398)
Q Consensus       265 ~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~  323 (398)
                      ++.+.|..+|+|.+..+.    .+...-+|.|+|......+-++.++|..+.-...++.
T Consensus       167 e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr~~gre~k~qhsr~a  221 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALRSHGRERKRQHSRRA  221 (479)
T ss_pred             hhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHHhcchhhhhhhhhhh
Confidence            999999999999977653    3333558889999888888889999988774443333

>KOG0106|consensus

Probab=98.44  E-value=1.8e-07  Score=80.71  Aligned_cols=71  Identities=23%  Similarity=0.542  Sum_probs=62.2

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      ..|||++|++.+.+.||.++|.+||.|.++.+.        .||+||+|++.-+| .++..+|++.|.|..+.|.|++.+
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            368999999999999999999999999988763        46999999996555 556689999999999999999864

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

Probab=98.43  E-value=1.3e-06  Score=66.04  Aligned_cols=60  Identities=15%  Similarity=0.293  Sum_probs=54.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcC--CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMF--GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~--G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      +||.|+|||...|.++|.+++...  |...-+.+..|..++.+.|||||.|.+.+.+.+..+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~   63 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYK   63 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHH
Confidence            699999999999999999988643  567778888898899999999999999999999876

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

>KOG2193|consensus

Probab=98.41  E-value=2.3e-08  Score=92.01  Aligned_cols=151  Identities=21%  Similarity=0.382  Sum_probs=116.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcC--CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCC-cccCCcccCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMF--GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPI-HTLDGKKIDPKHA  237 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~--G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~-~~~~g~~l~v~~~  237 (398)
                      ..+|++||...++.++|+.+|...  +.-..+ ++       -.||+||.+.+...+.++++ +++ ..+.|+++.+..+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f-l~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-ee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            468999999999999999999754  211122 11       25799999999999999998 444 4489999999888


Q ss_pred             CCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEee-cCCCCCcceEEEEEeCCHHHHH-HHHHHCCcee
Q psy6490         238 TPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM-DQQTKRHRGFGFVTFENEEVVD-HICEIHFHMI  315 (398)
Q Consensus       238 ~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~-~~~~~~~kg~afV~F~~~eaa~-a~~~l~~~~i  315 (398)
                      ..+..     .++++-|+|+|....++.|..++..||.++.|..+. |.++-    ..-|+|.+.+.++ ++..++|..+
T Consensus        74 v~kkq-----rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~eta----vvnvty~~~~~~~~ai~kl~g~Q~  144 (584)
T KOG2193|consen   74 VPKKQ-----RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETA----VVNVTYSAQQQHRQAIHKLNGPQL  144 (584)
T ss_pred             hhHHH-----HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHH----HHHHHHHHHHHHHHHHHhhcchHh
Confidence            76654     466799999999999999999999999999987643 32221    2236777766554 4557999999


Q ss_pred             CCEEEEEEecCchH
Q psy6490         316 KNKKVECKKAQPKE  329 (398)
Q Consensus       316 ~g~~i~v~~a~~k~  329 (398)
                      ....++|.|--...
T Consensus       145 en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  145 ENQHLKVGYIPDEQ  158 (584)
T ss_pred             hhhhhhcccCchhh
Confidence            99999999865443

>KOG4454|consensus

Probab=98.39  E-value=1.6e-07  Score=79.41  Aligned_cols=78  Identities=18%  Similarity=0.219  Sum_probs=66.9

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~a  325 (398)
                      +..++|||.|+...++||-|.++|-.-|.|.+|.|..++ .++.| ||||.|+++-++.-+++ +||..+.++.+.|.+.
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            456899999999999999999999999999999887774 56666 99999999887766664 7999999999888874


Q ss_pred             C
Q psy6490         326 Q  326 (398)
Q Consensus       326 ~  326 (398)
                      .
T Consensus        85 ~   85 (267)
T KOG4454|consen   85 C   85 (267)
T ss_pred             c
Confidence            3

>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=98.26  E-value=3e-06  Score=60.85  Aligned_cols=69  Identities=23%  Similarity=0.326  Sum_probs=47.2

Q ss_pred             cEEEEcCCCCCCCHHHH----HHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         162 AKLFVGGLSWQTSSEKL----REYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L----~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ..|||.|||.+.+...|    +.+++.|| +|.+|          +.+.|+|.|.+.+.|++|.+ +++..+.|++|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            57999999999887765    56677887 66665          24679999999999999998 88999999999998


Q ss_pred             CCCCC
Q psy6490         236 HATPK  240 (398)
Q Consensus       236 ~~~~~  240 (398)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            87543

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

>KOG0151|consensus

Probab=98.21  E-value=3.2e-06  Score=82.99  Aligned_cols=82  Identities=27%  Similarity=0.420  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCC---CCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP---ITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~---~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      +..+++|||+||+..++++.|...|..||.|.+++|+.-+   ...+.+.++||-|-+..++++|++ +++..+.++.++
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            5688999999999999999999999999999999998643   223456799999999999999998 899999999998


Q ss_pred             CCCCCC
Q psy6490         234 PKHATP  239 (398)
Q Consensus       234 v~~~~~  239 (398)
                      +.|.+.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            888754

>KOG0151|consensus

Probab=98.19  E-value=2.5e-06  Score=83.73  Aligned_cols=81  Identities=17%  Similarity=0.370  Sum_probs=69.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecC---CCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ---QTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~---~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ..++.|||+||+..++++.|...|..||.|..++|+.-.   +..+.+.|+||-|-+..++++++ +|+|..+.+..+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            346789999999999999999999999999999987532   33455779999999977776665 79999999999999


Q ss_pred             EecCc
Q psy6490         323 KKAQP  327 (398)
Q Consensus       323 ~~a~~  327 (398)
                      .|++.
T Consensus       252 gWgk~  256 (877)
T KOG0151|consen  252 GWGKA  256 (877)
T ss_pred             ccccc
Confidence            99843

>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=98.12  E-value=5.5e-06  Score=64.11  Aligned_cols=75  Identities=28%  Similarity=0.326  Sum_probs=44.8

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH---HC---CceeCCEEEEEE
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE---IH---FHMIKNKKVECK  323 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~---l~---~~~i~g~~i~v~  323 (398)
                      ..|+|.+++..++.++|+++|+.||.|.+|.+.+.      ...|||+|.+.++|+++++   ..   +..|.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            45889999999999999999999999999888654      2378999999887877664   23   567788888877


Q ss_pred             ecCchHH
Q psy6490         324 KAQPKEA  330 (398)
Q Consensus       324 ~a~~k~~  330 (398)
                      .-...++
T Consensus        76 vLeGeeE   82 (105)
T PF08777_consen   76 VLEGEEE   82 (105)
T ss_dssp             ---HHHH
T ss_pred             ECCCHHH
Confidence            7555443

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

>KOG1995|consensus

Probab=98.01  E-value=4.9e-06  Score=75.94  Aligned_cols=85  Identities=15%  Similarity=0.247  Sum_probs=74.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE--------TVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~--------v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      .....+|||-+|+..+++++|.++|..+|.|+.        |.|.+|++|+.+||-|.|.|+|..+|++++ .++++.+.
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            345668999999999999999999999998863        667889999999999999999988888876 58999999


Q ss_pred             CEEEEEEecCchHH
Q psy6490         317 NKKVECKKAQPKEA  330 (398)
Q Consensus       317 g~~i~v~~a~~k~~  330 (398)
                      +..|+|.++..+..
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999999876653

>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=97.89  E-value=5.1e-05  Score=54.63  Aligned_cols=68  Identities=12%  Similarity=0.225  Sum_probs=43.8

Q ss_pred             cceeecCCCCCCCHHH----HHHHHhhcCC-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         250 KKIFVGGVSQDTSAEE----VKAYFSQFGK-VEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~----L~~~F~~~G~-i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      ..|+|.|||.+.+...    |+.++..+|. |..|.          .+.|+|+|.+.|.|++++ .|+|..+-|++|.|+
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            4589999999988765    5566667874 44431          468999999988776655 799999999999999


Q ss_pred             ecCc
Q psy6490         324 KAQP  327 (398)
Q Consensus       324 ~a~~  327 (398)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9743

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

>KOG4849|consensus

Probab=97.88  E-value=1e-05  Score=73.08  Aligned_cols=79  Identities=18%  Similarity=0.401  Sum_probs=68.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCC--CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFG--AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G--~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      +....++|||||-+++|++||.+.+...|  .+.++++..++.+|.+||||+|...+..++++.++ +-..+|+|..-.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            44678999999999999999999998888  68889999999999999999999999999999998 5666788776544


Q ss_pred             CC
Q psy6490         235 KH  236 (398)
Q Consensus       235 ~~  236 (398)
                      ..
T Consensus       157 ~~  158 (498)
T KOG4849|consen  157 LS  158 (498)
T ss_pred             ec
Confidence            33

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.81  E-value=5e-05  Score=68.49  Aligned_cols=80  Identities=20%  Similarity=0.433  Sum_probs=60.3

Q ss_pred             ccceeecCCCCCCCHHHH------HHHHhhcCCeeEEEEeecCCCCCc-ceE--EEEEeCC-HHHHHHHHHHCCceeCCE
Q psy6490         249 TKKIFVGGVSQDTSAEEV------KAYFSQFGKVEETVMLMDQQTKRH-RGF--GFVTFEN-EEVVDHICEIHFHMIKNK  318 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L------~~~F~~~G~i~~v~i~~~~~~~~~-kg~--afV~F~~-~eaa~a~~~l~~~~i~g~  318 (398)
                      ..-+||-+|+..+-.|++      .++|..||.|..|.|-+......+ .+.  .||.|.+ +|+|+.+.+.+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            345899999998877762      479999999998887665322211 222  3999999 556666778999999999


Q ss_pred             EEEEEecCch
Q psy6490         319 KVECKKAQPK  328 (398)
Q Consensus       319 ~i~v~~a~~k  328 (398)
                      .|+..+...|
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999987764

>KOG1855|consensus

Probab=97.76  E-value=2.4e-05  Score=72.80  Aligned_cols=66  Identities=15%  Similarity=0.217  Sum_probs=54.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeec---CCC--CCc--------ceEEEEEeCCHHHHHHHHHHCC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD---QQT--KRH--------RGFGFVTFENEEVVDHICEIHF  312 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~---~~~--~~~--------kg~afV~F~~~eaa~a~~~l~~  312 (398)
                      -..++|.+.|||.+-.-|.|.++|+.+|.|+.|+|+.-   ..+  +.+        +-||||+|+..++|+++.++.+
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            46889999999999999999999999999999999875   222  222        4579999999999988887653

>KOG4210|consensus

Probab=97.76  E-value=2.4e-05  Score=71.78  Aligned_cols=83  Identities=23%  Similarity=0.476  Sum_probs=73.6

Q ss_pred             CCcEEE-EcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         160 TSAKLF-VGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~-v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ...++| |++|+.++++++|+..|..+|.|..+++..+..++.++||+||.|.+..+...++......+.++.+.+....
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDE  262 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCC
Confidence            445566 9999999999999999999999999999999999999999999999999999998876677888888888776


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      ....
T Consensus       263 ~~~~  266 (285)
T KOG4210|consen  263 PRPK  266 (285)
T ss_pred             CCcc
Confidence            6543

>KOG1995|consensus

Probab=97.73  E-value=6.4e-05  Score=68.78  Aligned_cols=84  Identities=15%  Similarity=0.293  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEE--------EEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD  228 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~  228 (398)
                      .....+|||-+|+..+++++|.++|.+||.|.        .|+|-+|+.|++.||-|.|.|.+...|+.|+. +++..+.
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            44778999999999999999999999999875        36777889999999999999999999999998 7888898


Q ss_pred             CcccCCCCCCCCC
Q psy6490         229 GKKIDPKHATPKN  241 (398)
Q Consensus       229 g~~l~v~~~~~~~  241 (398)
                      +..|.|..+..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            8888887766544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.67  E-value=5.8e-05  Score=68.08  Aligned_cols=111  Identities=18%  Similarity=0.356  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCCHHHH------HHHHhcCCCEEEEEEeeCCCCCC-cccE--EEEEEcChHhHHHHHh-CCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKL------REYFGMFGAVTDVLIMKDPITQR-SRGF--GFITFAEPETVEKVLK-VPIHTLDG  229 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L------~~~f~~~G~i~~~~~~~~~~~~~-~~g~--afV~f~~~e~a~~al~-~~~~~~~g  229 (398)
                      ...-+||-+|+..+-.+++      .++|.+||.|..|.+.+...+.. ..+.  .||.|.+.|+|.+||. .++..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            5577999999999887773      47899999999988766542111 1122  4999999999999998 89999999


Q ss_pred             cccCCCCCCCCC-----CCccCccccceeecCCC---CCCCHHHHHHHH
Q psy6490         230 KKIDPKHATPKN-----RPKIGNRTKKIFVGGVS---QDTSAEEVKAYF  270 (398)
Q Consensus       230 ~~l~v~~~~~~~-----~~~~~~~~~~l~V~nLp---~~~tee~L~~~F  270 (398)
                      |-|+..+...+-     +........++|+.--.   +..|++||-..=
T Consensus       193 r~lkatYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~q  241 (480)
T COG5175         193 RVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQ  241 (480)
T ss_pred             ceEeeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhhh
Confidence            999888776432     11222233445544332   246777775543

>KOG4849|consensus

Probab=97.64  E-value=3.6e-05  Score=69.69  Aligned_cols=78  Identities=12%  Similarity=0.255  Sum_probs=65.6

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEe
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKK  324 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G--~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~  324 (398)
                      +..++||+||-+.+|++||.+.+...|  .+.+++++.++.+|.+||||+|...++.+.+..++ |-.+.|.|..-.|--
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            345799999999999999999998766  47778888888899999999999999999999887 567778887666654


Q ss_pred             c
Q psy6490         325 A  325 (398)
Q Consensus       325 a  325 (398)
                      +
T Consensus       159 ~  159 (498)
T KOG4849|consen  159 Y  159 (498)
T ss_pred             c
Confidence            4

>KOG1996|consensus

Probab=97.63  E-value=0.00018  Score=63.83  Aligned_cols=80  Identities=13%  Similarity=0.205  Sum_probs=58.1

Q ss_pred             ceeecCC--CCCCC---HHHHHHHHhhcCCeeEEEEeecCCCCC-cceEEEEEeCCH-HHHHHHHHHCCceeCCEEEEEE
Q psy6490         251 KIFVGGV--SQDTS---AEEVKAYFSQFGKVEETVMLMDQQTKR-HRGFGFVTFENE-EVVDHICEIHFHMIKNKKVECK  323 (398)
Q Consensus       251 ~l~V~nL--p~~~t---ee~L~~~F~~~G~i~~v~i~~~~~~~~-~kg~afV~F~~~-eaa~a~~~l~~~~i~g~~i~v~  323 (398)
                      .|.++|+  +..++   ++++++.+++||.|.+|.|+.+..--. ..--.||+|++. ++.+|+..|||.+|+||.++..
T Consensus       283 vlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~  362 (378)
T KOG1996|consen  283 VLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSAC  362 (378)
T ss_pred             HHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehe
Confidence            3555554  22333   468899999999999999887642211 123579999995 5667888999999999999999


Q ss_pred             ecCchHH
Q psy6490         324 KAQPKEA  330 (398)
Q Consensus       324 ~a~~k~~  330 (398)
                      |......
T Consensus       363 Fyn~ekf  369 (378)
T KOG1996|consen  363 FYNLEKF  369 (378)
T ss_pred             eccHHhh
Confidence            8765443

>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=97.62  E-value=0.00018  Score=54.79  Aligned_cols=79  Identities=16%  Similarity=0.216  Sum_probs=53.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEe-ecC------CCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEE-
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML-MDQ------QTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKK-  319 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~-~~~------~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~-  319 (398)
                      ..+.|.|-+.|.. ....|.++|++||.|.+..-. ++.      .......+..|+|++..+|.+|+..||..|+|.. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            4566888898888 566788899999999876411 110      0012256999999999999999999999999864 


Q ss_pred             EEEEecCc
Q psy6490         320 VECKKAQP  327 (398)
Q Consensus       320 i~v~~a~~  327 (398)
                      +-|.++++
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            55777743

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.

>KOG3152|consensus

Probab=97.53  E-value=5e-05  Score=66.14  Aligned_cols=72  Identities=18%  Similarity=0.323  Sum_probs=59.2

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCC--------CCcce----EEEEEeCCHHHHHHHH-HHCCce
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT--------KRHRG----FGFVTFENEEVVDHIC-EIHFHM  314 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~--------~~~kg----~afV~F~~~eaa~a~~-~l~~~~  314 (398)
                      ....||+++||..++-..|+++|+.||.|-+|.+-....+        |.+++    .|+|+|.+...|+.+. .||+..
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            4567999999999999999999999999999998776544        22222    2679999988887765 689999


Q ss_pred             eCCEE
Q psy6490         315 IKNKK  319 (398)
Q Consensus       315 i~g~~  319 (398)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99975

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

Probab=97.51  E-value=0.00026  Score=47.35  Aligned_cols=52  Identities=23%  Similarity=0.447  Sum_probs=42.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHH
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL  220 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al  220 (398)
                      +.|-|.+.+.+..+. +++.|..||+|.++.+..      ...+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            578889998777755 555888999999988862      2458999999999999985

>KOG3152|consensus

Probab=97.49  E-value=7.4e-05  Score=65.12  Aligned_cols=73  Identities=15%  Similarity=0.318  Sum_probs=61.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCC--------CCcccE----EEEEEcChHhHHHHHh-CCCcc
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT--------QRSRGF----GFITFAEPETVEKVLK-VPIHT  226 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~--------~~~~g~----afV~f~~~e~a~~al~-~~~~~  226 (398)
                      .+..||+++||+.++-.-|+++|+.||.|-.|.+.....+        |.++++    |+|+|.+...|+++.. +|+.-
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            5689999999999999999999999999999999876554        333322    8899999999999877 78888


Q ss_pred             cCCccc
Q psy6490         227 LDGKKI  232 (398)
Q Consensus       227 ~~g~~l  232 (398)
                      |+|++-
T Consensus       153 Iggkk~  158 (278)
T KOG3152|consen  153 IGGKKK  158 (278)
T ss_pred             cCCCCC
Confidence            888753

>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=97.41  E-value=0.00035  Score=54.10  Aligned_cols=54  Identities=33%  Similarity=0.510  Sum_probs=36.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ..|+|.++...++.++|+++|+.||.|..|.+.+.      ...|||.|.+.++|++|++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~   55 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALE   55 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHH
Confidence            46889999999999999999999999999888664      2379999999999999987

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

>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=97.35  E-value=0.00063  Score=51.82  Aligned_cols=72  Identities=15%  Similarity=0.239  Sum_probs=50.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCC-------CCCCcccEEEEEEcChHhHHHHHhCCCcccCCccc
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-------ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI  232 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~-------~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l  232 (398)
                      ..+.|.|-+.|.+ ....|.+.|++||.|.+..-..+.       .......+-.|.|.++.+|.+||..|+..++|.-+
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            5577889999988 556688899999999887511100       00113568999999999999999999999988644

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.

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

Probab=97.34  E-value=0.00043  Score=46.30  Aligned_cols=52  Identities=19%  Similarity=0.376  Sum_probs=39.8

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC  308 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~  308 (398)
                      +.|-|.+.+.+.. ++|+++|..||+|.++.+-      ....+.||+|.+..+|+.|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            5678888887765 4556689999999998774      22458999999988877653

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.31  E-value=0.001  Score=53.82  Aligned_cols=57  Identities=18%  Similarity=0.278  Sum_probs=45.6

Q ss_pred             HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCch
Q psy6490         264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       264 e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      .+|.+.|..||+|.=+|++-+        .-+|+|.+-++|.+++.++|..++|+.|+|+...+.
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            367788889999887776544        569999999999999999999999999999986653

; PDB: 1UFW_A 2DNR_A.

>KOG2314|consensus

Probab=97.30  E-value=0.00051  Score=66.32  Aligned_cols=73  Identities=19%  Similarity=0.290  Sum_probs=57.1

Q ss_pred             CCCCCCCCcEEEEcCCCCCC--CHH----HHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcc
Q psy6490         154 PTGDDPTSAKLFVGGLSWQT--SSE----KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHT  226 (398)
Q Consensus       154 ~~~~~~~~~~l~v~nLp~~~--t~~----~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~  226 (398)
                      +..++.-...|+|.|+|---  .-+    -|..+|+++|+|.++.+..+..+| ++||.|++|.+..+|+.|++ +++..
T Consensus        51 p~~~eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~  129 (698)
T KOG2314|consen   51 PVTAEGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKR  129 (698)
T ss_pred             cCccCCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccce
Confidence            33445677899999998532  222    356789999999999999887655 99999999999999999998 45544


Q ss_pred             c
Q psy6490         227 L  227 (398)
Q Consensus       227 ~  227 (398)
                      |
T Consensus       130 l  130 (698)
T KOG2314|consen  130 L  130 (698)
T ss_pred             e
Confidence            4

>KOG0115|consensus

Probab=97.29  E-value=0.00027  Score=61.74  Aligned_cols=92  Identities=16%  Similarity=0.241  Sum_probs=70.5

Q ss_pred             CCCcccCCcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCH
Q psy6490         222 VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE  301 (398)
Q Consensus       222 ~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~  301 (398)
                      +++....|+.++|.++..          ..|||.||...++.|.|.+.|+.||.|+...++.| ..++..+-++|+|...
T Consensus        14 Ld~~~~~~~~lr~rfa~~----------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k   82 (275)
T KOG0115|consen   14 LDGRFPKGRSLRVRFAMH----------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKK   82 (275)
T ss_pred             cCCCCCCCCceEEEeecc----------ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcc
Confidence            557778888898888863          45999999999999999999999999999888888 4688889999999985


Q ss_pred             HHHHHHHH-H--C--CceeCCEEEEEEe
Q psy6490         302 EVVDHICE-I--H--FHMIKNKKVECKK  324 (398)
Q Consensus       302 eaa~a~~~-l--~--~~~i~g~~i~v~~  324 (398)
                      -.+.+++. .  .  +....++.+-|..
T Consensus        83 ~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   83 PNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             hhHHHHHHHhccCccccCCCCCccCCCh
Confidence            55544443 2  1  2233455555544

>KOG0129|consensus

Probab=97.27  E-value=0.00099  Score=63.93  Aligned_cols=64  Identities=30%  Similarity=0.445  Sum_probs=59.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHh-cCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~-~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      -+..+|||||+||.-++.++|-.+|+ -||.|..+-|=.|.+-+-.||-|-|.|.+..+-.+||.
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            45789999999999999999999999 89999999998887778899999999999999999986

>KOG2314|consensus

Probab=97.15  E-value=0.0007  Score=65.42  Aligned_cols=76  Identities=14%  Similarity=0.218  Sum_probs=58.0

Q ss_pred             cccceeecCCCCCC------CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeC-CEE
Q psy6490         248 RTKKIFVGGVSQDT------SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIK-NKK  319 (398)
Q Consensus       248 ~~~~l~V~nLp~~~------tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~-g~~  319 (398)
                      -...|+|.|+|---      -..-|.++|+++|+|..+.+..+.++| ++||.|++|.+...| +++.++||+.|+ ..+
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            45678999988632      224567899999999999998886554 999999999996655 566789999986 455


Q ss_pred             EEEEe
Q psy6490         320 VECKK  324 (398)
Q Consensus       320 i~v~~  324 (398)
                      ..|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            66654

>KOG1855|consensus

Probab=97.07  E-value=0.00068  Score=63.40  Aligned_cols=70  Identities=20%  Similarity=0.326  Sum_probs=57.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeC---CCC--CCc--------ccEEEEEEcChHhHHHHHhC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKD---PIT--QRS--------RGFGFITFAEPETVEKVLKV  222 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~---~~~--~~~--------~g~afV~f~~~e~a~~al~~  222 (398)
                      .++-.+++|.+-|||.+-..+.|.++|+.||.|..|+|..-   ..+  +..        +-+|+|+|+..+.|.+|.++
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34458999999999999999999999999999999999865   222  222        45699999999999999985


Q ss_pred             CCc
Q psy6490         223 PIH  225 (398)
Q Consensus       223 ~~~  225 (398)
                      .+.
T Consensus       306 ~~~  308 (484)
T KOG1855|consen  306 LNP  308 (484)
T ss_pred             hch
Confidence            433

>KOG2202|consensus

Probab=96.79  E-value=0.00063  Score=59.63  Aligned_cols=64  Identities=16%  Similarity=0.266  Sum_probs=50.0

Q ss_pred             HHHHHHHh-hcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         264 EEVKAYFS-QFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       264 e~L~~~F~-~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      |||...|+ +||+|++++|..+ -.-.-+|=+||.|..+|+|++++ .||+.++.|+.|...++.-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            55666666 8999999876544 33445788999999988777665 69999999999999987543

>KOG2253|consensus

Probab=96.76  E-value=0.00079  Score=66.46  Aligned_cols=109  Identities=15%  Similarity=0.136  Sum_probs=77.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +..+|||+||...+..+-++.++..||-|.+++...         |||++|.......+++. ++...++|.++.+....
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d~  109 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVDE  109 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccchh
Confidence            557999999999999999999999999998886643         99999999999999987 56667888877665421


Q ss_pred             CCCCC---------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCee
Q psy6490         239 PKNRP---------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE  277 (398)
Q Consensus       239 ~~~~~---------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~  277 (398)
                      .....               ......+-.+|.|++....+...+..|.--+...
T Consensus       110 q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~s~~  163 (668)
T KOG2253|consen  110 QTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQISSSAA  163 (668)
T ss_pred             hhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhccchhh
Confidence            11000               0011134467778877776666655555444333

>KOG4676|consensus

Probab=96.41  E-value=0.0046  Score=57.32  Aligned_cols=77  Identities=13%  Similarity=0.218  Sum_probs=64.1

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT---KRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~---~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ..|.|.||...+|.|.+..+|.-.|.|.++.++.....   ....-.|||.|.|..++..+..|-++.+=|+-|.|..+-
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            37899999999999999999999999999998763222   223458999999999999999998888888887776543

>KOG0112|consensus

Probab=96.36  E-value=0.0016  Score=66.33  Aligned_cols=80  Identities=24%  Similarity=0.381  Sum_probs=65.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ..+++||++||+..+++.+|+..|..||.|.+|.|.+-. -+...-|+||.|.+.+++ .+..++.+..|..-.+++.+.
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            356789999999999999999999999999999986553 233345999999997765 666789888888777777777


Q ss_pred             Cc
Q psy6490         326 QP  327 (398)
Q Consensus       326 ~~  327 (398)
                      .+
T Consensus       449 ~~  450 (975)
T KOG0112|consen  449 QP  450 (975)
T ss_pred             cc
Confidence            55

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

Probab=96.34  E-value=0.016  Score=42.01  Aligned_cols=54  Identities=17%  Similarity=0.342  Sum_probs=38.8

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI  310 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l  310 (398)
                      +....+|+ .|.++...||.++|+.||.|. |..+-|       .-|||...+.+.++.++.+
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~   61 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNT   61 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHH
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHH
Confidence            34455666 999999999999999999988 554444       2799999998888876653

; 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.

>KOG1924|consensus

Probab=96.23  E-value=0.023  Score=57.44  Aligned_cols=8  Identities=13%  Similarity=0.273  Sum_probs=4.0

Q ss_pred             CCcEEEEc
Q psy6490         160 TSAKLFVG  167 (398)
Q Consensus       160 ~~~~l~v~  167 (398)
                      ...+.||+
T Consensus       640 s~~cFWvk  647 (1102)
T KOG1924|consen  640 SENCFWVK  647 (1102)
T ss_pred             Cccceeee
Confidence            33455555

>KOG0115|consensus

Probab=96.21  E-value=0.015  Score=51.06  Aligned_cols=59  Identities=24%  Similarity=0.374  Sum_probs=53.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ..|||.||..-++.+.|..-|+.||.|....++.|. .++..+-++|+|...-.+.+|++
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~r   90 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAAR   90 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHH
Confidence            789999999999999999999999999887777764 67778889999999999988886

>KOG2135|consensus

Probab=96.20  E-value=0.0087  Score=56.94  Aligned_cols=70  Identities=16%  Similarity=0.224  Sum_probs=54.4

Q ss_pred             ecCCCCCC-CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCchH
Q psy6490         254 VGGVSQDT-SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       254 V~nLp~~~-tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      +.-.++.. |.++|..+|.+||+|..|-|-..      ---|.|+|.+...|-.+...++..|++|.|+|.|-++..
T Consensus       377 lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  377 LEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEEecCCc
Confidence            33334433 56899999999999999877433      236899999987776677779999999999999987644

>KOG1996|consensus

Probab=96.17  E-value=0.012  Score=52.56  Aligned_cols=62  Identities=18%  Similarity=0.261  Sum_probs=48.8

Q ss_pred             HHHHHHHhcCCCEEEEEEeeCCCCCCc-ccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         176 EKLREYFGMFGAVTDVLIMKDPITQRS-RGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       176 ~~L~~~f~~~G~i~~~~~~~~~~~~~~-~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      +++++-+++||.|.+|.|..+..--.. .--.||+|...++|.+|+- +|+.+|+||.+...+.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            567888999999999988876432222 2248999999999999986 8999999998865544

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.09  E-value=0.01  Score=48.05  Aligned_cols=72  Identities=21%  Similarity=0.298  Sum_probs=51.8

Q ss_pred             CCcEEEEcCCC------CCCCH---HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCc
Q psy6490         160 TSAKLFVGGLS------WQTSS---EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGK  230 (398)
Q Consensus       160 ~~~~l~v~nLp------~~~t~---~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~  230 (398)
                      ...||.|.=+.      ....+   .+|.+.|..||++.-+|++.+        .-+|+|.+-++|-+|+.+++..++|+
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~   97 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGR   97 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCE
Confidence            55677666554      12332   357778899999888877655        48999999999999999999999999


Q ss_pred             ccCCCCCCC
Q psy6490         231 KIDPKHATP  239 (398)
Q Consensus       231 ~l~v~~~~~  239 (398)
                      .|.|+...+
T Consensus        98 ~l~i~LKtp  106 (146)
T PF08952_consen   98 TLKIRLKTP  106 (146)
T ss_dssp             EEEEEE---
T ss_pred             EEEEEeCCc
Confidence            988765543

; PDB: 1UFW_A 2DNR_A.

>KOG2416|consensus

Probab=96.08  E-value=0.0081  Score=58.70  Aligned_cols=82  Identities=15%  Similarity=0.186  Sum_probs=63.0

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhh-cCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCcee---CCEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMI---KNKK  319 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~-~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i---~g~~  319 (398)
                      ....++.|||.||-.-+|.-.|+.++.+ .|.|++.+  +|+.    |..|||.|.+.+.| ...-.|||..+   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~W--mDkI----KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFW--MDKI----KSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHH--HHHh----hcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            4456778999999999999999999995 66677663  3422    55899999996555 44557888875   6899


Q ss_pred             EEEEecCchHHHh
Q psy6490         320 VECKKAQPKEAVQ  332 (398)
Q Consensus       320 i~v~~a~~k~~~~  332 (398)
                      |.+.|....+..+
T Consensus       514 L~adf~~~deld~  526 (718)
T KOG2416|consen  514 LIADFVRADELDK  526 (718)
T ss_pred             eEeeecchhHHHH
Confidence            9999988766553

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.77  E-value=0.056  Score=37.08  Aligned_cols=54  Identities=17%  Similarity=0.340  Sum_probs=44.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcC---CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMF---GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~---G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ....|+|+|+ .+++.++|+.+|..|   .....|..+.|.       .|-|.|.+.+.|.+||.
T Consensus         4 rpeavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    4 RPEAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALV   60 (62)
T ss_pred             eeceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHH
Confidence            3468999999 468899999999999   134567777774       58999999999999986

>KOG2202|consensus

Probab=95.76  E-value=0.0038  Score=54.82  Aligned_cols=61  Identities=13%  Similarity=0.259  Sum_probs=47.7

Q ss_pred             HHHHHh-cCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         178 LREYFG-MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       178 L~~~f~-~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      |...|+ +||+|+++++..+. .-.-+|-+||.|..+|+|++|+. +|+..++|+.|.......
T Consensus        85 ~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   85 VFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            333334 99999998775543 33467889999999999999998 899999999987766543

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

Probab=95.69  E-value=0.064  Score=38.90  Aligned_cols=53  Identities=13%  Similarity=0.307  Sum_probs=39.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      .....||+ .|.++...||.++|+.||.|. |..+.|.       .|||...+.+.+..+++
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHH
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHH
Confidence            44566666 999999999999999999876 4445543       79999999999998876

; 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.

>KOG2068|consensus

Probab=95.45  E-value=0.015  Score=53.25  Aligned_cols=110  Identities=22%  Similarity=0.403  Sum_probs=75.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHH---HHHhcCCCEEEEEEeeCCC--CCC-cccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         160 TSAKLFVGGLSWQTSSEKLR---EYFGMFGAVTDVLIMKDPI--TQR-SRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~---~~f~~~G~i~~~~~~~~~~--~~~-~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      ..+-+||-+|+..+.++++.   +.|..||.|..|.+.++..  .+. .-.-+||.|...|+|.+||. .++..++|+.+
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            45778999999887666654   5788999999998888762  111 12238999999999999998 78888999987


Q ss_pred             CCCCCCCCCC-----CccCccccceeecCCC---CCCCHHHHHHH
Q psy6490         233 DPKHATPKNR-----PKIGNRTKKIFVGGVS---QDTSAEEVKAY  269 (398)
Q Consensus       233 ~v~~~~~~~~-----~~~~~~~~~l~V~nLp---~~~tee~L~~~  269 (398)
                      +......+..     ........++|+.-+.   ..+|.+|++..
T Consensus       156 ka~~gttkycs~~l~~~~c~~~~cmylhe~~~~~Ds~~k~e~~~~  200 (327)
T KOG2068|consen  156 KASLGTTKYCSFYLRNDICQNPDCMYLHEIGDQEDSFTKDEMKSA  200 (327)
T ss_pred             HHhhCCCcchhHHhhhhcccCccccccccccccccccchHHHHHH
Confidence            7666554322     1222233457766553   34666666543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.43  E-value=0.09  Score=36.09  Aligned_cols=52  Identities=25%  Similarity=0.409  Sum_probs=39.2

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhc---CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQF---GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC  308 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~---G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~  308 (398)
                      ..+|+|+|+. +++-+||+.+|..|   ....+|..+-|.       -|-|.|.+.+.|.+++
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARAL   59 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHH
Confidence            4569999984 58889999999998   134457776663       5789999987776655

>KOG2416|consensus

Probab=95.22  E-value=0.011  Score=57.78  Aligned_cols=75  Identities=15%  Similarity=0.220  Sum_probs=57.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHh-cCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc---CCcc
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL---DGKK  231 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~-~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~---~g~~  231 (398)
                      -...++.|||.||-.-+|.-.|++++. .+|.|++.+|-+      -|..|||.|.+.++|..... |++..+   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            455789999999999999999999998 677777775532      35679999999999988776 555553   5555


Q ss_pred             cCCCCC
Q psy6490         232 IDPKHA  237 (398)
Q Consensus       232 l~v~~~  237 (398)
                      |.+.+.
T Consensus       514 L~adf~  519 (718)
T KOG2416|consen  514 LIADFV  519 (718)
T ss_pred             eEeeec
Confidence            655443

>KOG4285|consensus

Probab=95.08  E-value=0.08  Score=47.71  Aligned_cols=80  Identities=20%  Similarity=0.232  Sum_probs=58.6

Q ss_pred             CCCCCCCC--CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCc
Q psy6490         153 TPTGDDPT--SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGK  230 (398)
Q Consensus       153 ~~~~~~~~--~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~  230 (398)
                      .+.+++.+  +.-|-|-+++..-.. .|..+|++||+|++.....      .-.+-+|.|.+..+|.+||..++..|+|.
T Consensus       187 ~pte~~~d~~D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALskng~ii~g~  259 (350)
T KOG4285|consen  187 QPTEEEADAADTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALSKNGTIIDGD  259 (350)
T ss_pred             cccccccccccceEEEeccCccchh-HHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhhhcCeeeccc
Confidence            33444444  677778788876554 4677899999998776542      24589999999999999999999998886


Q ss_pred             c-cCCCCCCC
Q psy6490         231 K-IDPKHATP  239 (398)
Q Consensus       231 ~-l~v~~~~~  239 (398)
                      . |-|+.+.+
T Consensus       260 vmiGVkpCtD  269 (350)
T KOG4285|consen  260 VMIGVKPCTD  269 (350)
T ss_pred             eEEeeeecCC
Confidence            4 34555443

>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=95.03  E-value=0.27  Score=38.21  Aligned_cols=66  Identities=17%  Similarity=0.215  Sum_probs=46.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      .+..+.+...|..++.++|..+.+.+- .|..++|++|..  .++-.+++.|.+.++|+...+ .||+.+
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            445556666666677777877766664 677889988743  356679999999999999977 344443

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=94.97  E-value=0.076  Score=44.03  Aligned_cols=116  Identities=19%  Similarity=0.113  Sum_probs=78.0

Q ss_pred             cEEEEcCCC--CCCCHHHHHHHHhc-CCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         162 AKLFVGGLS--WQTSSEKLREYFGM-FGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       162 ~~l~v~nLp--~~~t~~~L~~~f~~-~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ....|+.+-  ...+-..|.+.+.+ .+....+.+..-     ..++..+.|.+.+++.++++...-.++|..+.+....
T Consensus        16 ~~~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l-----~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~   90 (153)
T PF14111_consen   16 QLCLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL-----GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWS   90 (153)
T ss_pred             CeEEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe-----CCCeEEEEEEeccceeEEEecccccccccchhhhhhc
Confidence            344455552  23556666665543 222223333222     3568999999999999999977777888888888777


Q ss_pred             CCCCCccC---ccccceeecCCCCC-CCHHHHHHHHhhcCCeeEEEEe
Q psy6490         239 PKNRPKIG---NRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVML  282 (398)
Q Consensus       239 ~~~~~~~~---~~~~~l~V~nLp~~-~tee~L~~~F~~~G~i~~v~i~  282 (398)
                      +.......   ...-.|.|.|||.. .+++-|+.+.+.+|.+.++...
T Consensus        91 ~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen   91 PDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             ccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence            54433222   23445888999987 6788889999999999987654

>KOG2068|consensus

Probab=94.96  E-value=0.011  Score=54.11  Aligned_cols=82  Identities=21%  Similarity=0.334  Sum_probs=60.3

Q ss_pred             cceeecCCCCCCCHHHHH---HHHhhcCCeeEEEEeecCC--CCC-cceEEEEEeCCH-HHHHHHHHHCCceeCCEEEEE
Q psy6490         250 KKIFVGGVSQDTSAEEVK---AYFSQFGKVEETVMLMDQQ--TKR-HRGFGFVTFENE-EVVDHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~---~~F~~~G~i~~v~i~~~~~--~~~-~kg~afV~F~~~-eaa~a~~~l~~~~i~g~~i~v  322 (398)
                      .-+||-+|+..+.++++.   +.|..||.|..|.+.++..  .+. ...-++|+|+.+ +++.++...+|..++|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            457888998877666654   4899999999999888752  111 111279999995 555666689999999999888


Q ss_pred             EecCchHHH
Q psy6490         323 KKAQPKEAV  331 (398)
Q Consensus       323 ~~a~~k~~~  331 (398)
                      .+...+-..
T Consensus       158 ~~gttkycs  166 (327)
T KOG2068|consen  158 SLGTTKYCS  166 (327)
T ss_pred             hhCCCcchh
Confidence            887776544

>KOG4285|consensus

Probab=94.94  E-value=0.071  Score=48.03  Aligned_cols=79  Identities=14%  Similarity=0.176  Sum_probs=61.3

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEE-EEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKK-VECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~-i~v~~a~~  327 (398)
                      ...|.|-+.+..-. .-|..+|++||.|.+...-      ..-.|-+|+|.+.-.|++++..||+.|+|.. |-|+.|..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCC
Confidence            45677778876543 4577889999999976543      2245999999999999999999999998764 67888888


Q ss_pred             hHHHhhh
Q psy6490         328 KEAVQAN  334 (398)
Q Consensus       328 k~~~~~~  334 (398)
                      |......
T Consensus       270 ksvi~~s  276 (350)
T KOG4285|consen  270 KSVINGS  276 (350)
T ss_pred             HHHhccc
Confidence            7766543

>KOG2135|consensus

Probab=94.86  E-value=0.017  Score=55.13  Aligned_cols=80  Identities=13%  Similarity=0.135  Sum_probs=66.9

Q ss_pred             CCCCCCcEEEEcCCCCCCC-HHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTS-SEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t-~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v  234 (398)
                      ....+.+.|-+.-++..+. -++|...|.+||+|.+|.+-..      .-.|.|+|.+..+|-+|...++..|+++.|.+
T Consensus       367 ~~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl  440 (526)
T KOG2135|consen  367 HAVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKL  440 (526)
T ss_pred             chhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEE
Confidence            3444677888888888864 4889999999999999988543      23699999999999999999999999999999


Q ss_pred             CCCCCCC
Q psy6490         235 KHATPKN  241 (398)
Q Consensus       235 ~~~~~~~  241 (398)
                      .|..+..
T Consensus       441 ~whnps~  447 (526)
T KOG2135|consen  441 FWHNPSP  447 (526)
T ss_pred             EEecCCc
Confidence            9988755

>KOG2193|consensus

Probab=94.74  E-value=0.045  Score=51.50  Aligned_cols=77  Identities=17%  Similarity=0.384  Sum_probs=57.2

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhc--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHH-HHHHHCCc-eeCCEEEEEEec
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQF--GKVEETVMLMDQQTKRHRGFGFVTFENEEVVD-HICEIHFH-MIKNKKVECKKA  325 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~--G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~-a~~~l~~~-~i~g~~i~v~~a  325 (398)
                      .++|++||...++..||+.+|...  +.-..+  +.      ..||+||.+.+..-+. ++..++|+ .+.|+++.|...
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f--l~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF--LV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce--ee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            468999999999999999999863  211111  11      1579999999977554 45557665 588999999999


Q ss_pred             CchHHHhhh
Q psy6490         326 QPKEAVQAN  334 (398)
Q Consensus       326 ~~k~~~~~~  334 (398)
                      .+|..+.+.
T Consensus        74 v~kkqrsrk   82 (584)
T KOG2193|consen   74 VPKKQRSRK   82 (584)
T ss_pred             hhHHHHhhh
Confidence            888766543

>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=94.46  E-value=0.036  Score=47.23  Aligned_cols=81  Identities=12%  Similarity=0.087  Sum_probs=47.1

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhh-cCCe---eEEEEeecCCC-C-CcceEEEEEeCCHHHHHHHH-HHCCceeCC---
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQ-FGKV---EETVMLMDQQT-K-RHRGFGFVTFENEEVVDHIC-EIHFHMIKN---  317 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~-~G~i---~~v~i~~~~~~-~-~~kg~afV~F~~~eaa~a~~-~l~~~~i~g---  317 (398)
                      ...+|.|++||..+||+++++.++. ++.-   .++.-...... . ..-..|||.|.+.+++.... .++|+.+-+   
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            4568999999999999999997776 6665   33331122111 1 12346999999977766655 678876632   


Q ss_pred             --EEEEEEecCch
Q psy6490         318 --KKVECKKAQPK  328 (398)
Q Consensus       318 --~~i~v~~a~~k  328 (398)
                        ....|++|--+
T Consensus        86 ~~~~~~VE~Apyq   98 (176)
T PF03467_consen   86 NEYPAVVEFAPYQ   98 (176)
T ss_dssp             -EEEEEEEE-SS-
T ss_pred             CCcceeEEEcchh
Confidence              35667776543

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.

>KOG2591|consensus

Probab=94.38  E-value=0.11  Score=50.72  Aligned_cols=71  Identities=17%  Similarity=0.214  Sum_probs=57.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHh--cCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh---CCCcccCCc
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFG--MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK---VPIHTLDGK  230 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~--~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~---~~~~~~~g~  230 (398)
                      ......+.|.++.||..+-+|+++.+|+  .|-++++|.+-.+.       -=||+|++.+||..|.+   ...++|.|+
T Consensus       170 rp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgK  242 (684)
T KOG2591|consen  170 RPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGK  242 (684)
T ss_pred             ccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCc
Confidence            3445678889999999999999999996  57899999887653       36999999999999987   244568888


Q ss_pred             ccC
Q psy6490         231 KID  233 (398)
Q Consensus       231 ~l~  233 (398)
                      .|.
T Consensus       243 pIm  245 (684)
T KOG2591|consen  243 PIM  245 (684)
T ss_pred             chh
Confidence            764

>KOG2591|consensus

Probab=94.36  E-value=0.1  Score=50.97  Aligned_cols=69  Identities=17%  Similarity=0.292  Sum_probs=48.6

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhh--cCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH---HCCceeCCEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQ--FGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE---IHFHMIKNKKVE  321 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~--~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~---l~~~~i~g~~i~  321 (398)
                      .+.+.|.|+-|+..+-+|+|+.+|+.  +-.+.+|.+..+      .+| ||+|+++.+|..+.+   -.-+.|-|+.|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N------~nW-yITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN------DNW-YITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec------Cce-EEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            34567899999999999999999985  778888887655      223 899999766644322   233445555544


Q ss_pred             E
Q psy6490         322 C  322 (398)
Q Consensus       322 v  322 (398)
                      .
T Consensus       246 A  246 (684)
T KOG2591|consen  246 A  246 (684)
T ss_pred             h
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=94.30  E-value=0.2  Score=35.98  Aligned_cols=59  Identities=17%  Similarity=0.245  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHHhhcCC-----eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         259 QDTSAEEVKAYFSQFGK-----VEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       259 ~~~tee~L~~~F~~~G~-----i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ..++..+|..++...+.     |-+|.|..+        |+||+-....+.+.+..|++..++|++|+|+.|
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--------FSFVEVPEEVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHHHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            46788899998887654     556666433        899999888777778889999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.05  E-value=0.14  Score=43.79  Aligned_cols=61  Identities=20%  Similarity=0.171  Sum_probs=42.2

Q ss_pred             CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHC--CceeCCEEEEEEecCch
Q psy6490         262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIH--FHMIKNKKVECKKAQPK  328 (398)
Q Consensus       262 tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~--~~~i~g~~i~v~~a~~k  328 (398)
                      ..+.|+++|..|+.+....+++.      -+-..|.|.+.++|.+++ .++  +..+.|..++|-++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45889999999999988877655      236789999977776666 578  89999999999998543

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.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=93.90  E-value=0.58  Score=36.39  Aligned_cols=75  Identities=12%  Similarity=0.146  Sum_probs=51.0

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhc-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC---EEEEEE
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQF-GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN---KKVECK  323 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~-G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g---~~i~v~  323 (398)
                      ...+.+...|+.++-++|..+.+.+ ..|..++|++|..  .++-.++++|.+.++|+... +.||+.++.   ..++|-
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            3345555566667777777666654 4577888888843  34657899999988887755 789998753   345554


Q ss_pred             ec
Q psy6490         324 KA  325 (398)
Q Consensus       324 ~a  325 (398)
                      |.
T Consensus        91 fV   92 (110)
T PF07576_consen   91 FV   92 (110)
T ss_pred             EE
Confidence            43

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.41  E-value=0.28  Score=39.39  Aligned_cols=74  Identities=15%  Similarity=0.233  Sum_probs=54.1

Q ss_pred             CCCCCcEEEEcCCCCCCCH-HH---HHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCccc
Q psy6490         157 DDPTSAKLFVGGLSWQTSS-EK---LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI  232 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~-~~---L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l  232 (398)
                      .+.+-.+|.|+=|..++.. +|   +...++.||+|.+|.+.-       +-.|.|.|+|..+|-+|+.......-|..+
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~  154 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTMF  154 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCceE
Confidence            4557789999877766533 44   445568999999998753       447999999999999999854555566666


Q ss_pred             CCCCC
Q psy6490         233 DPKHA  237 (398)
Q Consensus       233 ~v~~~  237 (398)
                      .+.|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            55553

>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=93.28  E-value=0.03  Score=41.47  Aligned_cols=66  Identities=20%  Similarity=0.276  Sum_probs=45.5

Q ss_pred             EEEEEcChHhHHHHHhC--CCcccCCcccCCCCCCC--CCC----CccCccccceeecCCCCCCCHHHHHHHHh
Q psy6490         206 GFITFAEPETVEKVLKV--PIHTLDGKKIDPKHATP--KNR----PKIGNRTKKIFVGGVSQDTSAEEVKAYFS  271 (398)
Q Consensus       206 afV~f~~~e~a~~al~~--~~~~~~g~~l~v~~~~~--~~~----~~~~~~~~~l~V~nLp~~~tee~L~~~F~  271 (398)
                      |+|+|.+.+-|++.+++  +...+++..+.|.....  ...    -...-..++|.|+|||..+++|+|++.++
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            68999999999999984  33446666655443221  111    11233567899999999999999988543

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>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=93.27  E-value=0.098  Score=44.58  Aligned_cols=69  Identities=13%  Similarity=0.098  Sum_probs=41.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhc-CCCEE---EEEEeeCCCC-C-CcccEEEEEEcChHhHHHHHh-CCCcccC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGM-FGAVT---DVLIMKDPIT-Q-RSRGFGFITFAEPETVEKVLK-VPIHTLD  228 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~-~G~i~---~~~~~~~~~~-~-~~~g~afV~f~~~e~a~~al~-~~~~~~~  228 (398)
                      ....|.|++||+++|++++.+.++. ++.-.   .+.-...... . ..-.-|||.|.+.+++..... +++..|.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            5579999999999999999987776 66552   2221122111 1 123359999999999888876 5665543

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.

>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=93.17  E-value=2.1  Score=38.84  Aligned_cols=168  Identities=9%  Similarity=0.146  Sum_probs=100.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCC-------CCCcccEEEEEEcChHhHHHHHh-----C--
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI-------TQRSRGFGFITFAEPETVEKVLK-----V--  222 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~-------~~~~~g~afV~f~~~e~a~~al~-----~--  222 (398)
                      +.-.+|.|.+.|+..+++--.+...|-+||.|++|.++.+..       ..+......+.|-+.+.+-....     +  
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            344789999999999999999999999999999999998751       12334578899999888765542     1  


Q ss_pred             CCcccCCcccCCCCCCCCCCC-----------------------ccCccccceeecCCCCCCCHHHHH-H---HHhhcC-
Q psy6490         223 PIHTLDGKKIDPKHATPKNRP-----------------------KIGNRTKKIFVGGVSQDTSAEEVK-A---YFSQFG-  274 (398)
Q Consensus       223 ~~~~~~g~~l~v~~~~~~~~~-----------------------~~~~~~~~l~V~nLp~~~tee~L~-~---~F~~~G-  274 (398)
                      -...++...|.+....-+...                       .....++.|.|. +...++++++. +   ++..-+ 
T Consensus        91 fK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL~~~~n  169 (309)
T PF10567_consen   91 FKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFLKNSNN  169 (309)
T ss_pred             HHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhhccCCC
Confidence            223355555544332210000                       011234455554 23444344332 2   222223 


Q ss_pred             ---CeeEEEEeecC--CCCCcceEEEEEeCCHHHHHHHHH---HCCceeC-CEEEEEEec
Q psy6490         275 ---KVEETVMLMDQ--QTKRHRGFGFVTFENEEVVDHICE---IHFHMIK-NKKVECKKA  325 (398)
Q Consensus       275 ---~i~~v~i~~~~--~~~~~kg~afV~F~~~eaa~a~~~---l~~~~i~-g~~i~v~~a  325 (398)
                         .|++|.|+.-.  ....++.||.+.|-+...|-.+++   .++...+ .+..-|...
T Consensus       170 ~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~  229 (309)
T PF10567_consen  170 KRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQ  229 (309)
T ss_pred             ceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEecc
Confidence               35666666432  234467899999999887766654   3444443 344444443

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.71  E-value=0.57  Score=37.67  Aligned_cols=72  Identities=15%  Similarity=0.244  Sum_probs=49.5

Q ss_pred             CccccceeecCCCCCCC-HHH---HHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHH-HHHHHHHHCCceeCCEEE
Q psy6490         246 GNRTKKIFVGGVSQDTS-AEE---VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICEIHFHMIKNKKV  320 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~t-ee~---L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~e-aa~a~~~l~~~~i~g~~i  320 (398)
                      ...-.+|.|+=|...+. .||   |...++.||.|.+|...     |  +--|.|.|+|.. +++|+...+. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            33456788876655542 234   44566779999998764     2  347999999954 5566666654 7778888


Q ss_pred             EEEec
Q psy6490         321 ECKKA  325 (398)
Q Consensus       321 ~v~~a  325 (398)
                      .+.|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            88885

>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=90.61  E-value=0.59  Score=32.61  Aligned_cols=52  Identities=13%  Similarity=0.228  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         172 QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       172 ~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      .++-++++..+.+|+- .  +|..|+     .| -||.|.+.++|++|.+ .++..+.+.+|
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~-----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m   63 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDR-----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRM   63 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecC-----CE-EEEEECChHHHHHHHHhcCCCEEEEEEE
Confidence            5788999999999963 2  334443     34 5899999999999998 45555555443

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804|consensus

Probab=90.13  E-value=1.1  Score=42.84  Aligned_cols=68  Identities=16%  Similarity=0.282  Sum_probs=56.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG  229 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g  229 (398)
                      .++.|+|-.+|..++-.||..|+..+- .|.++++++|...  ++=..++.|.+.++|....+ +||..|+.
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            389999999999999999999987664 7899999997432  34469999999999999987 66666654

>KOG3702|consensus

Probab=89.36  E-value=0.85  Score=45.81  Aligned_cols=72  Identities=8%  Similarity=0.077  Sum_probs=60.6

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEE
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v  322 (398)
                      +||+.|--..-+..-+..++..++.+...+++.....+..-+-++++|....+++++..+.++.+..+.+++
T Consensus       513 ~i~~~~~~~~s~~~s~s~~s~~~~~ltk~k~l~~Cky~~~Ct~a~Ce~~HPtaa~~~~s~p~k~fa~~~~ks  584 (681)
T KOG3702|consen  513 TIFVANGHGGSNPDSLSRHSEKKNELTKAKILTRCKYGPACTSAECEFAHPTAAENAKSLPNKKFASKCLKS  584 (681)
T ss_pred             ceecccccccCCCcchhhCcccccccccceeeccccCCCcCCchhhhhcCCcchhhhhccccccccccceec
Confidence            789988888888888999999999999999888877777666899999999998888887777777666555

>KOG2891|consensus

Probab=89.33  E-value=0.46  Score=42.40  Aligned_cols=38  Identities=21%  Similarity=0.501  Sum_probs=30.3

Q ss_pred             CccccceeecCCCCCC------------CHHHHHHHHhhcCCeeEEEEee
Q psy6490         246 GNRTKKIFVGGVSQDT------------SAEEVKAYFSQFGKVEETVMLM  283 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~------------tee~L~~~F~~~G~i~~v~i~~  283 (398)
                      .+...+|++.+||-.|            +++.|+..|+.||.|..|.|..
T Consensus       146 gerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipi  195 (445)
T KOG2891|consen  146 GERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPI  195 (445)
T ss_pred             CCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcc
Confidence            3456789998888543            6788999999999999988753

>KOG0804|consensus

Probab=88.81  E-value=1.1  Score=43.04  Aligned_cols=67  Identities=10%  Similarity=0.250  Sum_probs=54.6

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhc-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQF-GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN  317 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~-G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g  317 (398)
                      +..|+|-.+|-.+|-.||..|+..| -.|..++|++|...  ++=..+|+|.+.++|.... ++||+.|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            6789999999999999999999875 46899999997432  2445899999987777755 799998764

>KOG2253|consensus

Probab=88.32  E-value=0.26  Score=49.27  Aligned_cols=72  Identities=21%  Similarity=0.128  Sum_probs=59.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE-EVVDHICEIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~-eaa~a~~~l~~~~i~g~~i~v~  323 (398)
                      ......+|||+|+...+..+-++.+...+|.|.++..+.         |+|..|... -++++++.++-..++|..+.+.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            344567899999999999999999999999998776532         899999995 5667777888888988888776


Q ss_pred             ec
Q psy6490         324 KA  325 (398)
Q Consensus       324 ~a  325 (398)
                      .-
T Consensus       107 ~d  108 (668)
T KOG2253|consen  107 VD  108 (668)
T ss_pred             ch
Confidence            53

>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=88.15  E-value=0.79  Score=39.28  Aligned_cols=59  Identities=15%  Similarity=0.263  Sum_probs=42.8

Q ss_pred             CHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CC--CcccCCcccCCCCCC
Q psy6490         174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VP--IHTLDGKKIDPKHAT  238 (398)
Q Consensus       174 t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~--~~~~~g~~l~v~~~~  238 (398)
                      ..+.|+++|..|+.+..+..++.      -+-..|.|.+.++|.++.. ++  +..+.|..+++.+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            45789999999999988888765      3468999999999999987 56  677888888877663

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.

>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=84.11  E-value=5.6  Score=27.75  Aligned_cols=54  Identities=11%  Similarity=0.266  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         260 DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       260 ~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      .++-++++..+.+|+-..   |..| .    .|| ||.|.+.+.|+++. ..++..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~~---I~~d-~----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWDR---IRDD-R----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcce---EEec-C----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            578899999999997543   3334 2    345 89999977887776 46888887777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=83.91  E-value=1.4  Score=34.72  Aligned_cols=47  Identities=23%  Similarity=0.372  Sum_probs=28.2

Q ss_pred             CCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHH
Q psy6490         261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI  310 (398)
Q Consensus       261 ~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa~a~~~l  310 (398)
                      .+.++|++.|+.|..++ ++.+.+..  ...|+++|+|.+ -.--+.|+.+
T Consensus        29 ~~~~~l~~~l~~f~p~k-v~~l~~~~--gh~g~aiv~F~~~w~Gf~~A~~l   76 (116)
T PF03468_consen   29 MSNEELLDKLAEFNPLK-VKPLYGKQ--GHTGFAIVEFNKDWSGFKNAMRL   76 (116)
T ss_dssp             --SHHHHHHHHH---SE-EEEEEETT--EEEEEEEEE--SSHHHHHHHHHH
T ss_pred             cCHHHHHHHHHhcCCce-eEECcCCC--CCcEEEEEEECCChHHHHHHHHH
Confidence            45689999999999876 66666643  468999999986 4444444443

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.

>TIGR02542 B_forsyth_147 Bacteroides forsythus 147-residue repeat

Probab=83.69  E-value=2.2  Score=32.91  Aligned_cols=45  Identities=11%  Similarity=0.181  Sum_probs=31.0

Q ss_pred             CCCCCCHHHHHHHHhh---cCCeeEEEEeecCCCCCcceEEEEEeCCH
Q psy6490         257 VSQDTSAEEVKAYFSQ---FGKVEETVMLMDQQTKRHRGFGFVTFENE  301 (398)
Q Consensus       257 Lp~~~tee~L~~~F~~---~G~i~~v~i~~~~~~~~~kg~afV~F~~~  301 (398)
                      -|+.+|-.+|+++|++   |-.|.+-.+.+|---..+-..||..|...
T Consensus        82 ~PYTlT~~e~r~iF~Epm~YQGITReQV~rdGLP~GsYRiCFrL~~~~  129 (145)
T TIGR02542        82 PPYTLTYNELRQIFREPMVYQGITREQVQRDGLPEGSYRICFRLFNAT  129 (145)
T ss_pred             CceeeeHHHHHHHHhhhhhhccccHHHHhhcCCCCCceEEEEEEeccc
Confidence            4678999999999986   66666555555532223344788888753

The longest predicted protein in Bacteroides forsythus ATCC 43037 is over 3000 residues long and lacks homology to other known proteins. Immediately after the signal sequence are four tandem repeats, approximately 147 residues long. This model describes that repeat. This model describes that repeat.

>KOG4483|consensus

Probab=83.27  E-value=2.5  Score=39.94  Aligned_cols=58  Identities=14%  Similarity=0.173  Sum_probs=47.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCC-EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV  222 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~-i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~  222 (398)
                      .+-...|-|.++|.....+||...|+.|+. --+|+++-|.       .+|..|.+...|..||.+
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            335578999999999999999999999973 3455555553       799999999999999875

>KOG4410|consensus

Probab=83.16  E-value=3.8  Score=36.90  Aligned_cols=52  Identities=13%  Similarity=0.128  Sum_probs=37.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChH
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE  214 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e  214 (398)
                      ..-...||++||+.++.-.||+..+.+.|-+ -..+...    .+.|-||..|.+..
T Consensus       327 a~~~~di~~~nl~rd~rv~dlk~~lr~~~~~-pm~iswk----g~~~k~flh~~~~~  378 (396)
T KOG4410|consen  327 AGAKTDIKLTNLSRDIRVKDLKSELRKRECT-PMSISWK----GHFGKCFLHFGNRK  378 (396)
T ss_pred             CccccceeeccCccccchHHHHHHHHhcCCC-ceeEeee----cCCcceeEecCCcc
Confidence            3355679999999999999999999887632 1222222    14678999998753

>KOG2318|consensus

Probab=82.86  E-value=5.9  Score=39.43  Aligned_cols=126  Identities=13%  Similarity=0.211  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHhcC----CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCccc
Q psy6490         158 DPTSAKLFVGGLSWQ-TSSEKLREYFGMF----GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI  232 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~-~t~~~L~~~f~~~----G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l  232 (398)
                      ...+++|-|=||.++ +.-.+|.-+|+.|    |.|.+|.|....            |....-+       ...+.|-.+
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSe------------FGkeRM~-------eEeV~GP~~  231 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSE------------FGKERMK-------EEEVHGPPK  231 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhh------------hhHHHhh-------hhcccCChh
Confidence            447899999999987 7889999998866    588888886542            2221111       123444433


Q ss_pred             CCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHC
Q psy6490         233 DPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIH  311 (398)
Q Consensus       233 ~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~  311 (398)
                      .+...........           ...+..++-.+.-+..|+. .+.+.          =||.|+|.+.+.|.++. +++
T Consensus       232 el~~~~e~~~~s~-----------sD~ee~~~~~~~kLR~Yq~-~rLkY----------YyAVvecDsi~tA~~vYe~CD  289 (650)
T KOG2318|consen  232 ELFKPVEEYKESE-----------SDDEEEEDVDREKLRQYQL-NRLKY----------YYAVVECDSIETAKAVYEECD  289 (650)
T ss_pred             hhccccccCcccc-----------cchhhhhhHHHHHHHHHHh-hhhee----------EEEEEEecCchHHHHHHHhcC
Confidence            3322221111110           1111111222344444432 11111          18999999999999987 589


Q ss_pred             CceeCCE--EEEEEe
Q psy6490         312 FHMIKNK--KVECKK  324 (398)
Q Consensus       312 ~~~i~g~--~i~v~~  324 (398)
                      |..+...  .|.++|
T Consensus       290 G~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  290 GIEFESSANKLDLRF  304 (650)
T ss_pred             cceeccccceeeeee
Confidence            9988754  455554

>KOG4574|consensus

Probab=81.95  E-value=1  Score=46.54  Aligned_cols=77  Identities=12%  Similarity=0.115  Sum_probs=60.4

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HHHCCcee--CCEEEEEEecCch
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMI--KNKKVECKKAQPK  328 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~l~~~~i--~g~~i~v~~a~~k  328 (398)
                      .++.|..-..+-..|..+|+.||.|.+.+.+++.      ..|.|+|.+.+.|..+ ..++|+.+  -|-..+|.+++..
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            3455556677888999999999999999988883      3799999997766554 46888774  5778999999988


Q ss_pred             HHHhhh
Q psy6490         329 EAVQAN  334 (398)
Q Consensus       329 ~~~~~~  334 (398)
                      ++....
T Consensus       375 ~~~ep~  380 (1007)
T KOG4574|consen  375 PMYEPP  380 (1007)
T ss_pred             ccccCC
Confidence            776553

>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=80.57  E-value=2.4  Score=29.79  Aligned_cols=64  Identities=19%  Similarity=0.328  Sum_probs=48.1

Q ss_pred             HHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCCCC
Q psy6490         176 EKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN  241 (398)
Q Consensus       176 ~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~~~  241 (398)
                      ++|++-|...| .|.++.-+..+.++......||++....+...+++  -..+.+..+.|+....+.
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~i~~--Ik~l~~~~V~vE~~~k~~   66 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKEIYK--IKTLCGQRVKVERPRKRR   66 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccceee--hHhhCCeEEEEecCCCCC
Confidence            56788888888 78888888877677777789999988777555544  557888888887765443

These proteins are possibly involved in RNA binding or single strand DNA binding.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	398
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-44
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		8e-36
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		8e-12
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-36
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-12
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-36
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-11
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-35
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		4e-11
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-35
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-11
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-35
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-11
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		1e-25
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		1e-23
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-13
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		6e-23
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-12
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-20
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		8e-11
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-18
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-11
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-18
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		4e-10
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-17
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-16
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		3e-11
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		7e-15
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-14
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		7e-14
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-13
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-13
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		6e-13
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		7e-12
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		3e-11
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-08
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		2e-10
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		7e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-10
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-10
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-10
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		8e-10
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-10
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		9e-10
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-09
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		7e-09
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-08
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-08
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-06
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-08
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		9e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		4e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		4e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-05
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		7e-06
3d2w_A	89	Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Co		8e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-06
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		4e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		4e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		5e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		8e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		9e-05
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		1e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		2e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		8e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-04
3n9u_C	156	Crystal Structure Of The Complex Between The 25 Kda		4e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		4e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		4e-04
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		5e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		6e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		7e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score =  174 bits (442), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 79/168 (47%), Positives = 121/168 (72%), Gaps = 4/168 (2%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S K+F+GGL+W T+ + LREYFG +G VTD+ IMKDP T RSRGFGF++F +P +V++V+
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 221 KVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
           K   H LDGK IDPK A P++     ++T KIFVGG+  D   +E + +FSQ+G + +  
Sbjct: 63  KTQ-HILDGKVIDPKRAIPRDEQ---DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK 328
           +++D+ T + RGFGFVT+++ + VD +C+  F   K++K+E K+A+P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166

>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 =  147 bits (372), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 69/174 (39%), Positives = 109/174 (62%), Gaps = 3/174 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 223 PIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 76  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 135
Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+ + +
Sbjct: 136 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS 189

>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 = 68.2 bits (165), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 65/107 (60%), Gaps = 4/107 (3%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           PK   + +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E
Sbjct: 8   PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQ---ANLLVGKRVILGPL 346
            VD       H +  + VE K+A  +E  Q   A+L V K++ +G +
Sbjct: 68  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGI 113

>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 =  147 bits (371), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 69/174 (39%), Positives = 109/174 (62%), Gaps = 3/174 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 223 PIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 74  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 133
Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+ + +
Sbjct: 134 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS 187

>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 = 67.8 bits (164), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 65/107 (60%), Gaps = 4/107 (3%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           PK   + +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E
Sbjct: 6   PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQ---ANLLVGKRVILGPL 346
            VD       H +  + VE K+A  +E  Q   A+L V K++ +G +
Sbjct: 66  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGI 111

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score =  147 bits (371), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 69/174 (39%), Positives = 109/174 (62%), Gaps = 3/174 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 223 PIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+ + +
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS 188

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 65/107 (60%), Gaps = 4/107 (3%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           PK   + +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E
Sbjct: 7   PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQ---ANLLVGKRVILGPL 346
            VD       H +  + VE K+A  +E  Q   A+L V K++ +G +
Sbjct: 67  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGI 112

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score =  147 bits (370), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 69/174 (39%), Positives = 109/174 (62%), Gaps = 3/174 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 223 PIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127
Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+ + +
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS 181

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 37/100 (37%), Positives = 62/100 (62%), Gaps = 4/100 (4%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E VD    
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 310 IHFHMIKNKKVECKKAQPKEAVQ---ANLLVGKRVILGPL 346
              H +  + VE K+A  +E  Q   A+L V K++ +G +
Sbjct: 67  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGI 105

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score =  146 bits (369), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 69/170 (40%), Positives = 107/170 (62%), Gaps = 3/170 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 223 PIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 73  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 132
Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+
Sbjct: 133 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 182

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 65/107 (60%), Gaps = 4/107 (3%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           PK   + +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E
Sbjct: 5   PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQ---ANLLVGKRVILGPL 346
            VD       H +  + VE K+A  +E  Q   A+L V K++ +G +
Sbjct: 65  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGI 110

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score =  146 bits (369), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 69/170 (40%), Positives = 107/170 (62%), Gaps = 3/170 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 223 PIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 65/107 (60%), Gaps = 4/107 (3%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           PK   + +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E
Sbjct: 7   PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQ---ANLLVGKRVILGPL 346
            VD       H +  + VE K+A  +E  Q   A+L V K++ +G +
Sbjct: 67  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGI 112

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score =  114 bits (284), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 47/74 (63%), Positives = 62/74 (83%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           IFVGG+S +T+ E+VK YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEIH
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 312 FHMIKNKKVECKKA 325
           FH I NK VECKKA
Sbjct: 62  FHEINNKMVECKKA 75

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score =  107 bits (266), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 47/82 (57%), Positives = 60/82 (73%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +  K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KV
Sbjct: 24  SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
Query: 220 LKVPIHTLDGKKIDPKHATPKN 241
           L    H LD K IDPK A P+ 
Sbjct: 84  LAQSRHELDSKTIDPKVAFPRR 105

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 73.6 bits (179), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/86 (40%), Positives = 56/86 (65%)
Query: 245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV 304
           +G+   K+F+GG+S  T+ E ++ YF QFG+V+E +++ D  TKR RGFGFVTF ++  V
Sbjct: 21  MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Query: 305 DHICEIHFHMIKNKKVECKKAQPKEA 330
           D +     H + +K ++ K A P+ A
Sbjct: 81  DKVLAQSRHELDSKTIDPKVAFPRRA 106

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score =  105 bits (261), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 46/75 (61%), Positives = 57/75 (76%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 223 PIHTLDGKKIDPKHA 237
             H LD K IDPK A
Sbjct: 62  SRHELDSKTIDPKVA 76

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 69.7 bits (169), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 32/75 (42%), Positives = 50/75 (66%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S  T+ E ++ YF QFG+V+E +++ D  TKR RGFGFVTF ++  VD +   
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 311 HFHMIKNKKVECKKA 325
             H + +K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 52/79 (65%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            KLFVGGL W T+ E LR YF  +G V D +IMKD  T +SRGFGF+ F +P  V  VL 
Sbjct: 17  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 222 VPIHTLDGKKIDPKHATPK 240
              HTLDG+ IDPK  TP+
Sbjct: 77  SRPHTLDGRNIDPKPCTPR 95

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 64.7 bits (156), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 48/78 (61%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVGG+   T+ E +++YFSQ+G+V + V++ D+ T + RGFGFV F++   V  +   
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 311 HFHMIKNKKVECKKAQPK 328
             H +  + ++ K   P+
Sbjct: 78  RPHTLDGRNIDPKPCTPR 95

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 90.5 bits (223), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/74 (54%), Positives = 52/74 (70%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +F+GGLSW T+ + L++YF  FG V D  +  DPIT RSRGFGF+ F E E+V+KV+   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 224 IHTLDGKKIDPKHA 237
            H L+GK IDPK A
Sbjct: 62  EHKLNGKVIDPKRA 75

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 49/74 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +F+GG+S DT+ +++K YFS+FG+V +  + +D  T R RGFGFV F+  E VD + +  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 312 FHMIKNKKVECKKA 325
            H +  K ++ K+A
Sbjct: 62  EHKLNGKVIDPKRA 75

>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 = 90.5 bits (223), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/81 (54%), Positives = 53/81 (65%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           ++  + K FVGGLSW TS + L++YF  FG V D  I  DP T RSRGFGFI F +  +V
Sbjct: 7   NEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASV 66
Query: 217 EKVLKVPIHTLDGKKIDPKHA 237
           EKVL    H LDG+ IDPK A
Sbjct: 67  EKVLDQKEHRLDGRVIDPKKA 87

>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 = 62.4 bits (150), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 48/75 (64%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K FVGG+S DTS +++K YF++FG+V +  +  D  T R RGFGF+ F++   V+ + + 
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 311 HFHMIKNKKVECKKA 325
             H +  + ++ KKA
Sbjct: 73  KEHRLDGRVIDPKKA 87

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 87.4 bits (215), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 39/80 (48%), Positives = 56/80 (70%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+  +    E++ YF +FG V E VM+ D + +R RGFGF+TFE+E+ VD    +
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 311 HFHMIKNKKVECKKAQPKEA 330
           HFH I  KKVE K+A+P+++
Sbjct: 72  HFHDIMGKKVEVKRAEPRDS 91

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 84.0 bits (206), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 35/84 (41%), Positives = 57/84 (67%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR Y+  +G +TD ++M+DP ++RSRGFGF+TF+    V+  +  
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 223 PIHTLDGKKIDPKHATPKNRPKIG 246
             H++DG+ ++PK A  +     G
Sbjct: 89  RPHSIDGRVVEPKRAVAREESGSG 112

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 51/80 (63%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+F+GG+S +T+ E ++ Y+ Q+GK+ + V++ D  +KR RGFGFVTF +   VD    
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 310 IHFHMIKNKKVECKKAQPKE 329
              H I  + VE K+A  +E
Sbjct: 88  ARPHSIDGRVVEPKRAVARE 107

>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 = 78.2 bits (191), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 47/203 (23%), Positives = 96/203 (47%), Gaps = 14/203 (6%)
Query: 135 AHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM 194
           +H   +  G+  G    +   G     ++++VG + ++   + +R+ F  FG +  + + 
Sbjct: 2   SHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61
Query: 195 KDPITQRSRGFGFITFAEPETVEKVL-KVPIHTLDGKKIDPKHATPKN----RPKIGNRT 249
            D +T + +GF F+ +  PE  +  L ++    L G+ I  K   P N    +P I    
Sbjct: 62  WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI--KVGRPSNIGQAQPIIDQLA 119
Query: 250 K------KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
           +      +I+V  V QD S +++K+ F  FGK++   +  D  T +H+G+GF+ +E  + 
Sbjct: 120 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179
Query: 304 V-DHICEIHFHMIKNKKVECKKA 325
             D +  ++   +  + +   KA
Sbjct: 180 SQDAVSSMNLFDLGGQYLRVGKA 202

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 75.5 bits (184), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 44/147 (29%), Positives = 78/147 (53%), Gaps = 10/147 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L    + ++ +  FG  G +    +++D IT +S G+GF+ +++P   +K     
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA---- 62
Query: 224 IHTLDGKKIDPKH-ATPKNRPKIGN-RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM 281
           I+TL+G K+  K       RP   + R   ++V G+ +  S +E++  FSQ+G++  + +
Sbjct: 63  INTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 282 LMDQQTKRHRGFGFVTF----ENEEVV 304
           L+DQ T   RG GF+ F    E EE +
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAI 149

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 75.1 bits (183), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 45/147 (30%), Positives = 78/147 (53%), Gaps = 10/147 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L    + E+ R  FG  G +    +++D IT +S G+GF+ + +P+  EK     
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK----A 60
Query: 224 IHTLDGKKIDPKH-ATPKNRPKIGN-RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM 281
           I+TL+G ++  K       RP   + R   ++V G+ +  + +E++  FSQ+G++  + +
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 282 LMDQQTKRHRGFGFVTF----ENEEVV 304
           L+DQ T   RG GF+ F    E EE +
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAI 147

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 78/152 (51%), Gaps = 13/152 (8%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL- 220
            +++VG + ++   + +R+ F  FG +  + +  D +T + +GF F+ +  PE  +  L 
Sbjct: 14  CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 221 KVPIHTLDGKKIDPKHATPKN----RPKIGNRTK------KIFVGGVSQDTSAEEVKAYF 270
           ++    L G+ I  K   P N    +P I    +      +I+V  V QD S +++K+ F
Sbjct: 74  QMNSVMLGGRNI--KVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 131
Query: 271 SQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             FGK++   +  D  T +H+G+GF+ +E  +
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQ 163

>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 = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 76/152 (50%), Gaps = 13/152 (8%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            +++VG + ++   + +R+ F  FG +  +    D +T + +GF F+ +  PE  +  L+
Sbjct: 13  CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 222 VPIHT-LDGKKIDPKHATPKN----RPKIGNRTK------KIFVGGVSQDTSAEEVKAYF 270
                 L G+ I  K   P N    +P I    +      +I+V  V QD S +++K+ F
Sbjct: 73  QXNSVXLGGRNI--KVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 130
Query: 271 SQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             FGK++   +  D  T +H+G+GF+ +E  +
Sbjct: 131 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQ 162

>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 = 72.0 bits (175), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/76 (47%), Positives = 48/76 (63%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           KKIFVGG+S DT  E+++ YF  FG+VE   + MD +T + RGF F+TF+ EE V  I E
Sbjct: 2   KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 310 IHFHMIKNKKVECKKA 325
             +H +   K E K A
Sbjct: 62  KKYHNVGLSKCEIKVA 77

>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 = 68.2 bits (165), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 34/74 (45%), Positives = 46/74 (62%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           IFVGG+S DT  E+++ YF  FG+VE   + MD +T + RGF F+TF+ EE V  I E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 312 FHMIKNKKVECKKA 325
           +H +   K E K A
Sbjct: 62  YHNVGLSKCEIKVA 75

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/87 (36%), Positives = 51/87 (58%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           D T  K+FVGGL + T+   LR+YF  FG + + +++ D  T +SRG+GF+T A+    E
Sbjct: 14  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRPK 244
           +  K P   +DG+K +   A    +P+
Sbjct: 74  RACKDPNPIIDGRKANVNLAYLGAKPR 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 = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 42/75 (56%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+   T+   ++ YF  FG +EE V++ D+QT + RG+GFVT  +    +  C+ 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 311 HFHMIKNKKVECKKA 325
              +I  +K     A
Sbjct: 79  PNPIIDGRKANVNLA 93

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 37/89 (41%), Positives = 49/89 (55%), Gaps = 1/89 (1%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S        ++ L V GL W+T+ + L+EYF  FG V  V + KD  T  S+GFG
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK 235
           F+ F E ET  KV+    H +DG+  D K
Sbjct: 61  FVRFTEYETQVKVMS-QRHMIDGRWCDCK 88

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
            +T  + V G+   T+ +++K YFS FG+V    +  D +T   +GFGFV F   E    
Sbjct: 13  QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72
Query: 307 ICEIHFHMIKNKKVECKKAQPKEA 330
           +     HMI  +  +CK    K++
Sbjct: 73  VMS-QRHMIDGRWCDCKLPNSKQS 95

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/75 (41%), Positives = 50/75 (66%), Gaps = 4/75 (5%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            KLFVGGLS+ T+ + L + F  +G +++V+++KD  TQRSRGFGF+TF   E ++   K
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF---ENIDDA-K 68
Query: 222 VPIHTLDGKKIDPKH 236
             +  ++GK +D + 
Sbjct: 69  DAMMAMNGKSVDGRQ 83

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 26/50 (52%), Positives = 41/50 (82%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           K+FVGG+S DT+ + ++  FS++G++ E V++ D++T+R RGFGFVTFEN
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

>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 = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/191 (24%), Positives = 88/191 (46%), Gaps = 11/191 (5%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G   P+      A L+VG L    +   L E F   G +  + + +D IT+RS G+ ++ 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Query: 210 FAEPETVEKVLK-VPIHTLDGK--KIDPKHATPKNRPK-IGNRTKKIFVGGVSQDTSAEE 265
           F +P   E+ L  +    + GK  +I      P  R   +GN    IF+  + +    + 
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN----IFIKNLDKSIDNKA 119
Query: 266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKK 324
           +   FS FG +    ++ D+     +G+GFV FE +E  +   E ++  ++ ++KV   +
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 325 AQPKEAVQANL 335
            + ++  +A L
Sbjct: 178 FKSRKEREAEL 188

>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 = 61.6 bits (148), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 45/179 (25%), Positives = 85/179 (47%), Gaps = 11/179 (6%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+VG L    +   L E F   G +  + + +D IT+RS G+ ++ F +P   E+ L 
Sbjct: 11  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 222 -VPIHTLDGK--KIDPKHATPKNRPK-IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE 277
            +    + GK  +I      P  R   +GN    IF+  + +    + +   FS FG + 
Sbjct: 71  TMNFDVIKGKPVRIMWSQRDPSLRKSGVGN----IFIKNLDKSIDNKALYDTFSAFGNIL 126
Query: 278 ETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKAQPKEAVQANL 335
              ++ D+     +G+GFV FE +E  +   E ++  ++ ++KV   + + ++  +A L
Sbjct: 127 SCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 35/141 (24%), Positives = 71/141 (50%), Gaps = 12/141 (8%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L    + ++LR  F   G V    +++D +   S G+GF+ +   +  E+     
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER----A 60
Query: 224 IHTLDGKKIDPK-----HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
           I+TL+G ++  K     +A P +      +   +++ G+ +  + ++V+  FS+FG++  
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVI---KDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 279 TVMLMDQQTKRHRGFGFVTFE 299
           + +L+DQ T   RG  F+ F+
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFD 138

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 74/150 (49%), Gaps = 16/150 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L    + ++LR  F   G V    +++D +   S G+GF+ +   +  E+     
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER----A 60
Query: 224 IHTLDGKKIDPK-----HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
           I+TL+G ++  K     +A P +      +   +++ G+ +  + ++V+  FS+FG++  
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVI---KDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 279 TVMLMDQQTKRHRGFGFVTF----ENEEVV 304
           + +L+DQ T   RG  F+ F    E EE +
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147

>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 = 60.1 bits (144), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 50/83 (60%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           + I+VG +    ++E+VK  FSQFGKV    ++ D++TK+ +GFGFV  + E V + I +
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 310 IHFHMIKNKKVECKKAQPKEAVQ 332
           +       + +   +A PK++++
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLE 84

>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 = 58.2 bits (139), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 76/153 (49%), Gaps = 13/153 (8%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ--RSRGFGFITFA 211
           P   D  + K+FVG +    S + LRE F  +GAV ++ +++D      +S+G  F+TF 
Sbjct: 8   PDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFY 67
Query: 212 EPETVEKVLKVPIHTLDGKKIDP-KHATPKNRPKIGNRT-----KKIFVGGVSQDTSAEE 265
              T +  L+   + L   K+ P  H   + +P    +      +K+F+G +S+  +  +
Sbjct: 68  ---TRKAALEAQ-NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTEND 123
Query: 266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
           ++  FS FG++EE  +L        RG  FVTF
Sbjct: 124 IRVMFSSFGQIEECRILRGPDG-LSRGCAFVTF 155

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 72/144 (50%), Gaps = 13/144 (9%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ--RSRGFGFITFAEPETVEKVL 220
           K FVG +    S + LRE F  +GAV ++ +++D      +S+G  F+TF    T +  L
Sbjct: 5   KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFY---TRKAAL 61
Query: 221 KVPIHTLDGKKIDP-KHATPKNRPKIGNRT-----KKIFVGGVSQDTSAEEVKAYFSQFG 274
           +   + L   K+ P  H   + +P    +      +K+F+G +S+  +  +++  FS FG
Sbjct: 62  EAQ-NALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFG 120
Query: 275 KVEETVMLMDQQTKRHRGFGFVTF 298
           ++EE  +L        RG  FVTF
Sbjct: 121 QIEECRILRGPDG-LSRGCAFVTF 143

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
           KLF+GGL+ +T+ + L+  FG  G +++VL++KD  T +SRGF FITF  P   +   K 
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 222 VPIHTLDGKKIDPKHA 237
           +   +L GK I  + A
Sbjct: 68  MNGKSLHGKAIKVEQA 83

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 37/50 (74%), Gaps = 1/50 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           K+F+GG++++T+ + +KA F + G + E V+L+  +T + RGF F+TFEN
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISE-VLLIKDRTSKSRGFAFITFEN 57

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 73/144 (50%), Gaps = 13/144 (9%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ--RSRGFGFITFAEPETVEKVL 220
           K+FVG +    S + LRE F  +GAV ++ +++D      +S+G  F+TF    T +  L
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFY---TRKAAL 61
Query: 221 KVPIHTLDGKKIDP-KHATPKNRPKIGNRT-----KKIFVGGVSQDTSAEEVKAYFSQFG 274
           +   + L   K+ P  H   + +P    +      +K+F+G +S+  +  +++  FS FG
Sbjct: 62  EAQ-NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120
Query: 275 KVEETVMLMDQQTKRHRGFGFVTF 298
           ++EE  +L        RG  FVTF
Sbjct: 121 QIEECRILRGPDG-LSRGCAFVTF 143

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 54.7 bits (130), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 33/143 (23%), Positives = 71/143 (49%), Gaps = 9/143 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+VG L    + + L++YF + G + ++ IM D    ++  + F+ + +         + 
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDA----NIA 57
Query: 224 IHTLDGKKIDPK----HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
           + TL+GK+I+      +   +++    + T  +FVG ++ +   E ++  F  F      
Sbjct: 58  LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG 117
Query: 280 VMLMDQQTKRHRGFGFVTFENEE 302
            ++ D QT   RG+GFV+F +++
Sbjct: 118 HVMWDMQTGSSRGYGFVSFTSQD 140

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 40/61 (65%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S+ L+VG L +  + + LR  F  FG + ++++MKD  T RS+G+GFITF++ E   + L
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 221 K 221
           +
Sbjct: 65  E 65

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 32/51 (62%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++VG +  + + + ++  F  FGK++  V++ D  T R +G+GF+TF + E
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-K 221
           +L+VG L +  + + LR  F  FG +  + +M D  T RS+G+GFITF++ E  +K L +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 222 VPIHTLDGKKIDPKHATPK 240
           +    L G+ +   H T +
Sbjct: 88  LNGFELAGRPMKVGHVTER 106

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 35/59 (59%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +++VG +  + + + ++  F  FG++E   ++MD +T R +G+GF+TF + E      E
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 45/140 (32%), Positives = 67/140 (47%), Gaps = 21/140 (15%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
            +LFVG L    + E  +  F  +G  ++V I +D      RGFGFI   E  T+ ++ K
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRL-ESRTLAEIAK 75
Query: 222 VPIHTLDGKKIDPKHATPKNRP---KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
                LDG  +       K+RP   +       + V  +S   S E ++  FSQFG VE+
Sbjct: 76  A---ELDGTIL-------KSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEK 125
Query: 279 TVMLMDQQTKRHRGFGFVTF 298
            V+++D +  R  G GFV F
Sbjct: 126 AVVVVDDRG-RATGKGFVEF 144

>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 = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 1/95 (1%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    D      +FVG LS + ++E ++  F  FG ++D  ++KD  T +S+G+G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 207 FITFAEPETVEKVL-KVPIHTLDGKKIDPKHATPK 240
           F++F      E  + ++    L G++I    AT K
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 50/89 (56%), Gaps = 6/89 (6%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE-EVVDHICEI 310
           +FVG +S + + E++KA F+ FG++ +  ++ D  T + +G+GFV+F N+ +  + I ++
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 311 HFHMIKNKKVECKKA-----QPKEAVQAN 334
               +  +++    A      PK   ++N
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYESN 106

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 1/95 (1%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    D      +FVG LS + ++E ++  F  FG ++D  ++KD  T +S+G+G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 207 FITFAEPETVEK-VLKVPIHTLDGKKIDPKHATPK 240
           F++F      E  ++ +    L G++I    AT K
Sbjct: 61  FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE-EVVDHICEI 310
           +FVG +S + + E++K+ F+ FGK+ +  ++ D  T + +G+GFV+F N+ +  + I  +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 311 HFHMIKNKKVECKKAQPK 328
               +  +++    A  K
Sbjct: 78  GGQWLGGRQIRTNWATRK 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 = 50.8 bits (120), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/90 (40%), Positives = 48/90 (53%), Gaps = 6/90 (6%)
Query: 145 SSGDSG-RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
           SSG SG R+ P   DP    L V GLS  T+   LRE F  +G + DV I+ D  ++RSR
Sbjct: 2   SSGSSGNRANP---DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 57
Query: 204 GFGFITFAEPETV-EKVLKVPIHTLDGKKI 232
           GF F+ F   +   E   +     LDG++I
Sbjct: 58  GFAFVYFENVDDAKEAKERANGMELDGRRI 87

>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 = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV FEN
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
           G+ S   GR  P  +  TS K  V  L+++TS + LR  F  +G V DV I +D  T+ S
Sbjct: 31  GRGSMSYGRPPPDVEGMTSLK--VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES 88
Query: 203 RGFGFITFAEPETVEKVLK-VPIHTLDGKKI 232
           RGF F+ F +    E  +  +    LDG+++
Sbjct: 89  RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/90 (40%), Positives = 48/90 (53%), Gaps = 6/90 (6%)
Query: 145 SSGDSG-RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
           SSG SG R+ P   DP    L V GLS  T+   LRE F  +G + DV I+ D  ++RSR
Sbjct: 2   SSGSSGNRANP---DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 57
Query: 204 GFGFITFAEPETV-EKVLKVPIHTLDGKKI 232
           GF F+ F   +   E   +     LDG++I
Sbjct: 58  GFAFVYFENVDDAKEAKERANGMELDGRRI 87

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV FEN
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/104 (32%), Positives = 50/104 (48%), Gaps = 2/104 (1%)
Query: 131 VVREAHQLVLVNGKSSGDSGRSTPTGDDPT-SAKLFVGGLSWQTSSEKLREYFGMFGAVT 189
           V R +H   +  G+  G   R      +P  +  L V GLS  T+   LRE F  +G + 
Sbjct: 15  VPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIA 74
Query: 190 DVLIMKDPITQRSRGFGFITFAEPETV-EKVLKVPIHTLDGKKI 232
           DV I+ D  ++RSRGF F+ F   +   E   +     LDG++I
Sbjct: 75  DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/61 (36%), Positives = 37/61 (60%), Gaps = 5/61 (8%)
Query: 245 IGNRTKK-----IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           +GNR        + V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV FE
Sbjct: 37  VGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
Query: 300 N 300
           N
Sbjct: 97  N 97

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 4/90 (4%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ---RSRGFGFITFAEPETVE 217
           S+ LF+  L++ T+ E L+  F   GA+    I K         S GFGF+ + +PE  +
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 218 KVLK-VPIHTLDGKKIDPKHATPKNRPKIG 246
           K LK +  HT+DG K++ + +    +P  G
Sbjct: 65  KALKQLQGHTVDGHKLEVRISERATKPASG 94

>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex Wit Length = 89

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+FVG  ++D +AEE++ +F Q+G+V +  +      K  R F FVTF +++V   +C  
Sbjct: 13  KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDKVAQSLCGE 67
Query: 311 HFHMIKNKKVECKKAQPK 328
              +IK   V    A+PK
Sbjct: 68  DL-IIKGISVHISNAEPK 84

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 32/144 (22%), Positives = 63/144 (43%), Gaps = 4/144 (2%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           ++  L V  L    +  +L   F   G +    IM+D  T  S G+ F+ F      ++ 
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 220 LKVPIH-TLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
           +KV    T+  K++   +A P        +   ++V  + +  + +++   F ++G + +
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESI---KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 279 TVMLMDQQTKRHRGFGFVTFENEE 302
             +L D+ T R RG  FV +   E
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKRE 142

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 3/64 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-- 309
           +FVGG+       E++++F+++G V+E  ++ D +T   +G+GFV+F N+  V  I E  
Sbjct: 13  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 310 IHFH 313
           I+FH
Sbjct: 72  INFH 75

>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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 3/64 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-- 309
           +FVGG+       E++++F+++G V+E  ++ D +T   +G+GFV+F N+  V  I E  
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 310 IHFH 313
           I+FH
Sbjct: 71  INFH 74

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 3/64 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-- 309
           +FVGG+       E++++F+++G V+E  ++ D +T   +G+GFV+F N+  V  I E  
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 310 IHFH 313
           I+FH
Sbjct: 71  INFH 74

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
           L V  L+++TS + LR  F  +G V DV I +D  T+ SRGF F+ F +    E  +  +
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 223 PIHTLDGKKI 232
               LDG+++
Sbjct: 133 DGAVLDGREL 142

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 246 GNRTKKI-FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           G+ TK++ +VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E
Sbjct: 1   GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 58

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/83 (37%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           R+ P   DP    L V GLS  T+   LRE F  +G + DV I+ D  ++RSRGF F+ F
Sbjct: 6   RANP---DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 61
Query: 211 AEPETV-EKVLKVPIHTLDGKKI 232
              +   E   +     LDG++I
Sbjct: 62  ENVDDAKEAKERANGMELDGRRI 84

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV FEN
Sbjct: 17  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 38/74 (51%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P      +A + V  LS  T    L+E F  FG+++ + + KD  T +S+GF 
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 207 FITFAEPETVEKVL 220
           FI+F   E   + +
Sbjct: 61  FISFHRREDAARAI 74

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 46/96 (47%), Gaps = 6/96 (6%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P      S  LFV GLS  T+ E L+E F   G+V    I+ D  T  S+GFG
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFG 57
Query: 207 FITFAEPETVEKVLKVPIHT--LDGKKIDPKHATPK 240
           F+ F   E   K  K  +    +DG K+    A PK
Sbjct: 58  FVDFNSEEDA-KAAKEAMEDGEIDGNKVTLDWAKPK 92

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
           +K +FV G+S+DT+ E +K  F   G V   + + D++T   +GFGFV F +EE      
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFD--GSVRARI-VTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 309 E-IHFHMIKNKKVECKKAQPK 328
           E +    I   KV    A+PK
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPK 92

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P  D   + K  V  L+++TS + LR  F  +G V DV I ++P T+  RGF 
Sbjct: 1   GSSGSSGPDVDGMITLK--VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58
Query: 207 FITF 210
           F+ F
Sbjct: 59  FVRF 62

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           N+   ++VGG+ +  S   +   F Q G V  T M  D+ T +H+G+GFV F +EE  D+
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 307 ICEIHFHMIK--NKKVECKKA 325
             +I   MIK   K +   KA
Sbjct: 73  AIKI-MDMIKLYGKPIRVNKA 92

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 249 TKKI-FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           TK++ +VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 33/51 (64%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 55

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 5/92 (5%)
Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           G +  +  ++VG + +  ++E+L  +F   G+V  V I+ D  +   +GF +I F++ E+
Sbjct: 1   GXEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
Query: 216 VEKVLKVPIHTLDGKKID--PKHATPKNRPKI 245
           V   L +      G++I   PK     NRP I
Sbjct: 61  VRTSLALDESLFRGRQIKVIPKRT---NRPGI 89

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           +FVG  + D + +E++ +FSQ+G V +  +      K  R F FVTF ++++   +C   
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCGED 62
Query: 312 FHMIKNKKVECKKAQPK 328
             +IK   V    A+PK
Sbjct: 63  L-IIKGISVHISNAEPK 78

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 33/52 (63%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
           +LFV  LS+ +S E L + F  +G ++++    D +T++ +GF F+TF  PE
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG +T      T   L+VGGL+ +   + L   F  FG +TD+ I  D  T++ RG
Sbjct: 2   SSGSSGMAT------TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 55
Query: 205 FGFITFAEPE 214
           F F+ F   E
Sbjct: 56  FAFVEFELAE 65

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 249 TKKI-FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           TK++ +VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           ++VG + +  ++E+L  +F   G+V  V I+ D  +   +GF +I F++ E+V   L + 
Sbjct: 8   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 224 IHTLDGKKID--PKHATPKNRPKI 245
                G++I   PK     NRP I
Sbjct: 68  ESLFRGRQIKVIPKRT---NRPGI 88

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           + I+VG V    +AEE++A+F   G V    +L D+ +   +GF ++ F ++E V     
Sbjct: 6   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLL 336
           +   + + +++   K  PK   +  +L
Sbjct: 66  LDESLFRGRQI---KVIPKRTNRPGIL 89

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 249 TKKI-FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           TK++ +VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE
Sbjct: 62  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113

>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 = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 36/60 (60%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           P +    + +FVG +  + + E++K  FS+ G V    ++ D++T + +G+GF  ++++E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +   L V  L    + ++ +  FG  G +    +++D IT +S G+GF+ +++P   +K 
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 220 LKVPIHTLDGKKIDPK 235
               I+TL+G K+  K
Sbjct: 63  ----INTLNGLKLQTK 74

>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda Subunit And The 59 Kda Subunit (Rrm Domain) Of Human Cleavage Factor Im Length = 156

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 55/103 (53%), Gaps = 5/103 (4%)
Query: 153 TPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMK---DPITQRSRGFGFIT 209
           T +G     A ++VG  SW T+ ++L +     G V DV+ +K   +    +S+G+  + 
Sbjct: 47  TYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIG-VYDVVELKFAENRANGQSKGYAEVV 105
Query: 210 FAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
            A   +V K+L+ +P   L+G+K+D + AT +N  +   + +K
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARK 148

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           P+ + ++V  L +  ++  L   F  +G V  V IMKD  T++S+G  FI F + ++ +
Sbjct: 14  PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 150 GRSTPTGDDPTS---AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G S  +GD  T      L+V  L      E+LR+ F  FG +T   +M +    RS+GFG
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58
Query: 207 FITFAEPETVEKVL 220
           F+ F+ PE   K +
Sbjct: 59  FVCFSSPEEATKAV 72

>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 = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 32/52 (61%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K+F+G + ++   +++K  F +FGK+ E  +L D+ T  H+G  F+T+   E
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE 66

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           T  +L V  + ++     LR+ FG FG + DV I+ +   + S+GFGF+TF      ++ 
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRA 71
Query: 220 L-KVPIHTLDGKKIDPKHATPK 240
             K+    ++G+KI+  +AT +
Sbjct: 72  REKLHGTVVEGRKIEVNNATAR 93

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 5/80 (6%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           +L V  + ++     LR+ FG FG + DV I+ +   + S+GFGF+TF      ++  + 
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRA-RE 87
Query: 223 PIH--TLDGKKIDPKHATPK 240
            +H   ++G+KI+  +AT +
Sbjct: 88  KLHGTVVEGRKIEVNNATAR 107

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	398
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-92
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-34
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-91
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-37
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-30
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-62
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-18
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-51
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-34
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-47
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-46
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-46
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-19
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-45
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-35
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-44
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-39
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-44
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-35
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-43
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-43
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-36
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-42
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-33
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-42
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-34
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-42
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-39
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-42
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-42
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-40
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-21
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-40
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-38
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	7e-39
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-38
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-37
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-35
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-34
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-14
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-34
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-34
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-33
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-33
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-33
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-30
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-22
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-29
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-29
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-28
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-20
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-27
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-20
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-27
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-26
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-26
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-26
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-26
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-19
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-24
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-24
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-24
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-16
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-24
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-24
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-24
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-17
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-24
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-24
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-23
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-19
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-23
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-20
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-23
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-13
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-19
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-23
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-15
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-23
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-18
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-23
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-22
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-22
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-22
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-17
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-22
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-16
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-22
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-17
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-22
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-21
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-21
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-21
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-14
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-21
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-16
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-21
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-20
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-20
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-20
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-17
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-20
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-15
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-20
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-20
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-16
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-20
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-20
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	8e-20
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-20
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	9e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-14
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-19
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	6e-19
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-13
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-19
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-18
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-18
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-13
2div_A	99	TRNA selenocysteine associated protein; structural	2e-18
2div_A	99	TRNA selenocysteine associated protein; structural	1e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-18
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-18
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-18
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-15
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	9e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-17
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-17
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-17
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-14
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-17
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-17
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-16
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-16
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-16
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-13
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-16
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-13
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-14
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	8e-14
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-13
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-13
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-12
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-13
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	8e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-11
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-11
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-11
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-11
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	9e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-11
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-10
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-10
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	7e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-10
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-08
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-04

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  275 bits (706), Expect = 1e-92
 Identities = 70/185 (37%), Positives = 111/185 (60%), Gaps = 3/185 (1%)

Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
           +S    +     KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+
Sbjct: 3   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62

Query: 211 AEPETVEKVLKVPIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVK 267
           A  E V+  +    H +DG+ ++PK A  +    RP      KKIFVGG+ +DT    ++
Sbjct: 63  ATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 122

Query: 268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP 327
            YF Q+GK+E   ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS 182

Query: 328 KEAVQ 332
           K+ + 
Sbjct: 183 KQEMA 187

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  125 bits (317), Expect = 1e-34
 Identities = 32/111 (28%), Positives = 56/111 (50%)

Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
           V  K +     S   G   T  K+FVGG+   T    LR+YF  +G +  + IM D  + 
Sbjct: 84  VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSG 143

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
           + RGF F+TF + ++V+K++    HT++G   + + A  K      + +++
Sbjct: 144 KKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQR 194

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  271 bits (695), Expect = 3e-91
 Identities = 79/168 (47%), Positives = 121/168 (72%), Gaps = 4/168 (2%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S K+F+GGL+W T+ + LREYFG +G VTD+ IMKDP T RSRGFGF++F +P +V++V+
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62

Query: 221 KVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
           K   H LDGK IDPK A P++     ++T KIFVGG+  D   +E + +FSQ+G + +  
Sbjct: 63  KTQ-HILDGKVIDPKRAIPRDEQ---DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118

Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK 328
           +++D+ T + RGFGFVT+++ + VD +C+  F   K++K+E K+A+P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  132 bits (334), Expect = 2e-37
 Identities = 35/112 (31%), Positives = 59/112 (52%), Gaps = 4/112 (3%)

Query: 130 NVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT 189
            VV+  H L   +GK   D  R+ P  +   + K+FVGG+      ++  E+F  +G + 
Sbjct: 60  EVVKTQHIL---DGKVI-DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTII 115

Query: 190 DVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN 241
           D  +M D  T +SRGFGF+T+   + V++V +        +KI+ K A P++
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 167

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  113 bits (286), Expect = 2e-30
 Identities = 27/82 (32%), Positives = 52/82 (63%), Gaps = 1/82 (1%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
            + K+F+GG++ DT+ + ++ YF ++G V +  ++ D  T R RGFGF++FE    VD +
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
            +   H++  K ++ K+A P++
Sbjct: 62  VK-TQHILDGKVIDPKRAIPRD 82

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

 Score =  198 bits (506), Expect = 3e-62
 Identities = 40/199 (20%), Positives = 89/199 (44%), Gaps = 10/199 (5%)

Query: 140 LVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT 199
           +  G+  G    +   G     ++++VG + ++   + +R+ F  FG +  + +  D +T
Sbjct: 7   MTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 66

Query: 200 QRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNR--------PKIGNRTK 250
            + +GF F+ +  PE  +  L+ +    L G+ I     +   +         +      
Sbjct: 67  MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN 126

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           +I+V  V QD S +++K+ F  FGK++   +  D  T +H+G+GF+ +E  +     +  
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186

Query: 310 IHFHMIKNKKVECKKAQPK 328
           ++   +  + +   KA   
Sbjct: 187 MNLFDLGGQYLRVGKAVTP 205

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  174 bits (443), Expect = 2e-53
 Identities = 26/173 (15%), Positives = 70/173 (40%), Gaps = 9/173 (5%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-----IMKDPITQRSRGFGFITFAEP 213
            ++ +L+VG + +  + E + ++F     +  +       +      + + F F+ F   
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 214 ETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQF 273
           +   + +        G+ +  +               K+F+GG+    + ++VK   + F
Sbjct: 62  DETTQAMAFDGIIFQGQSLKIRRPHDYQPL---PGAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 274 GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKA 325
           G ++   ++ D  T   +G+ F  + +  V D     ++   + +KK+  ++A
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 96.5 bits (241), Expect = 5e-24
 Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 1/90 (1%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
            R       P + KLF+GGL    + ++++E    FG +    ++KD  T  S+G+ F  
Sbjct: 83  RRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 210 FAEPETVEKVL-KVPIHTLDGKKIDPKHAT 238
           + +    ++ +  +    L  KK+  + A+
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 81.1 bits (201), Expect = 2e-18
 Identities = 10/96 (10%), Positives = 37/96 (38%), Gaps = 7/96 (7%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML-----MDQQTKRHRGFGFVTFENEEVV 304
           ++++VG +    + E +  +F+   ++           +  Q  + + F F+ F + +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 305 DHICEIHFHMIKNKKVECKKAQPKEAVQ--ANLLVG 338
                    + + + ++ ++    + +     L +G
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIG 100

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  165 bits (421), Expect = 5e-51
 Identities = 41/114 (35%), Positives = 60/114 (52%), Gaps = 1/114 (0%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG      D  T  K+FVGGL + T+   LR+YF  FG + + +++ D  T +SRG
Sbjct: 2   SSGSSGMHGSQKD-TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVS 258
           +GF+T A+    E+  K P   +DG+K +   A    +P+       I V G S
Sbjct: 61  YGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPS 114

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  121 bits (305), Expect = 8e-34
 Identities = 29/109 (26%), Positives = 51/109 (46%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
           ++  +  +      KIFVGG+   T+   ++ YF  FG +EE V++ D+QT + RG+GFV
Sbjct: 5   SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64

Query: 297 TFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
           T  +    +  C+    +I  +K     A      ++        + GP
Sbjct: 65  TMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  157 bits (399), Expect = 7e-47
 Identities = 42/180 (23%), Positives = 76/180 (42%), Gaps = 19/180 (10%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT--QRSRGFGFITFAEPET 215
           D    K+FVG +    S + LRE F  +GAV ++ +++D      +S+G  F+TF   + 
Sbjct: 2   DAI--KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59

Query: 216 VEKVLKVPIHTLDGKKIDPKHATP------KNRPKIGNRTKKIFVGGVSQDTSAEEVKAY 269
             +      + L   K+ P    P       +        +K+F+G +S+  +  +++  
Sbjct: 60  ALEA----QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVM 115

Query: 270 FSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVDHICEIHFHMIKNKKVECKKA 325
           FS FG++EE  +L        RG  FVTF         +  + +       +  +  K A
Sbjct: 116 FSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  156 bits (396), Expect = 1e-46
 Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 9/171 (5%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +   L V  L    + E+ R  FG  G +    +++D IT +S G+GF+ + +P+  EK 
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 220 LKVPIH--TLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE 277
           +   ++   L  K I   +A P +      R   ++V G+ +  + +E++  FSQ+G++ 
Sbjct: 61  INT-LNGLRLQTKTIKVSYARPSSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116

Query: 278 ETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI---HFHMIKNKKVECKKA 325
            + +L+DQ T   RG GF+ F+     +   +           + +  K A
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 86.1 bits (214), Expect = 3e-20
 Identities = 31/117 (26%), Positives = 52/117 (44%), Gaps = 12/117 (10%)

Query: 117 DDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSE 176
            DP  A+  +  LN +R   + + V+         + P+      A L+V GL    + +
Sbjct: 52  IDPKDAEKAINTLNGLRLQTKTIKVS--------YARPSSASIRDANLYVSGLPKTMTQK 103

Query: 177 KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
           +L + F  +G +    I+ D +T  SRG GFI F +    E+     I  L+G+K  
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA----IKGLNGQKPS 156

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  155 bits (395), Expect = 3e-46
 Identities = 34/179 (18%), Positives = 71/179 (39%), Gaps = 8/179 (4%)

Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
                 +  T   LF+G L+   S  +L+       A  D+ ++ D  T  +R FG++ F
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDF 61

Query: 211 AEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYF 270
              E +EK L++    + G +I  +    +   K     + +    +S + + +E+K  F
Sbjct: 62  ESAEDLEKALELTGLKVFGNEIKLEKPKGR-DSKKVRAARTLLAKNLSFNITEDELKEVF 120

Query: 271 SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
               ++      +  Q  + +G  ++ F++E   +  + E     I  + V       K
Sbjct: 121 EDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 83.8 bits (208), Expect = 2e-19
 Identities = 20/107 (18%), Positives = 48/107 (44%), Gaps = 8/107 (7%)

Query: 236 HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF 295
           H    +          +F+G ++ + S  E+K   S+     +  + +D +T  +R FG+
Sbjct: 3   HMVEGSES---TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGY 58

Query: 296 VTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA----NLLVG 338
           V FE+ E ++   E+    +   +++ +K + +++ +      LL  
Sbjct: 59  VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAK 105

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score =  151 bits (384), Expect = 1e-45
 Identities = 51/105 (48%), Positives = 62/105 (59%), Gaps = 2/105 (1%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG +    D+    KLFVGGL W T+ E LR YF  +G V D +IMKD  T +SRG
Sbjct: 2   SSGSSGMNNSGADEIG--KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG 59

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
           FGF+ F +P  V  VL    HTLDG+ IDPK  TP+     G  +
Sbjct: 60  FGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSGPSS 104

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score =  124 bits (314), Expect = 3e-35
 Identities = 27/94 (28%), Positives = 50/94 (53%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
                 +   K+FVGG+   T+ E +++YFSQ+G+V + V++ D+ T + RGFGFV F++
Sbjct: 8   MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
              V  +     H +  + ++ K   P+    + 
Sbjct: 68  PNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSG 101

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score =  148 bits (377), Expect = 1e-44
 Identities = 52/100 (52%), Positives = 66/100 (66%), Gaps = 3/100 (3%)

Query: 148 DSGRSTPTGD--DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
            S    P G     +  K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGF
Sbjct: 10  HSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGF 69

Query: 206 GFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPK-NRPK 244
           GF+TF +   V+KVL    H LD K IDPK A P+  +PK
Sbjct: 70  GFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score =  135 bits (342), Expect = 2e-39
 Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 6/106 (5%)

Query: 225 HTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD 284
           H      + P+         +G+   K+F+GG+S  T+ E ++ YF QFG+V+E +++ D
Sbjct: 7   HHHHSSGLVPR------GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60

Query: 285 QQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEA 330
             TKR RGFGFVTF ++  VD +     H + +K ++ K A P+ A
Sbjct: 61  PLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA 106

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  148 bits (375), Expect = 3e-44
 Identities = 38/98 (38%), Positives = 50/98 (51%), Gaps = 1/98 (1%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S        ++ L V GL W+T+ + L+EYF  FG V  V + KD  T  S+GFG
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPK 244
           F+ F E ET  KV+    H +DG+  D K    K    
Sbjct: 61  FVRFTEYETQVKVMSQR-HMIDGRWCDCKLPNSKQSQD 97

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  125 bits (315), Expect = 2e-35
 Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 1/94 (1%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
              +   +T  + V G+   T+ +++K YFS FG+V    +  D +T   +GFGFV F  
Sbjct: 7   GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66

Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
            E    +     HMI  +  +CK    K++  + 
Sbjct: 67  YETQVKVMS-QRHMIDGRWCDCKLPNSKQSQDSG 99

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  151 bits (384), Expect = 3e-43
 Identities = 27/184 (14%), Positives = 61/184 (33%), Gaps = 12/184 (6%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           PT A L V  L    + ++  E    FG++    ++    T +S+G+GF  + + ++  +
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 219 VLKVPIHTLDGKKIDPKH-----ATPKNRPKIGNRTKKIFVGGVSQD-TSAEEVKAYFSQ 272
                   L GK + P+                  ++ + V  +       + +    S 
Sbjct: 153 A----KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSA 208

Query: 273 FGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKEAV 331
                   +    Q  + +GF  + +E  E   +   +     +    +      P    
Sbjct: 209 VHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

Query: 332 QANL 335
           ++ L
Sbjct: 268 RSML 271

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  123 bits (311), Expect = 9e-33
 Identities = 20/180 (11%), Positives = 63/180 (35%), Gaps = 16/180 (8%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
                 K+ + GL    +++++ +    +        +K     + +G  F+T    E  
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQA 70

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV 276
           E  +          ++  +  + + +P        + V  +    + ++ +     FG +
Sbjct: 71  EAAIN----AFHQSRLRERELSVQLQPTDAL----LCVANLPPSLTQQQFEELVRPFGSL 122

Query: 277 EETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
           E   ++  ++T + +G+GF  +  ++       ++    +  + +        +   A L
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 69.2 bits (170), Expect = 2e-13
 Identities = 17/113 (15%), Positives = 28/113 (24%), Gaps = 18/113 (15%)

Query: 142 NGKSSGDS----GRSTPTGDDPTSAK---LFVGGLSWQ-TSSEKLREYFGMFGAVTDVLI 193
            GK  G        +      P       L V  L       + L        + T   +
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQL 217

Query: 194 MKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH-----ATPKN 241
                  + +GF  + +   E  E+  +      DG  +   H       P  
Sbjct: 218 ACGQ-DGQLKGFAVLEYETAEMAEEAQQ----QADGLSLGGSHLRVSFCAPGP 265

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

 Score =  144 bits (366), Expect = 7e-43
 Identities = 35/99 (35%), Positives = 59/99 (59%)

Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
                 +     KLF+GGLS++T+ E LR Y+  +G +TD ++M+DP ++RSRGFGF+TF
Sbjct: 17  LERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76

Query: 211 AEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
           +    V+  +    H++DG+ ++PK A  +     G  +
Sbjct: 77  SSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSGPSS 115

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

 Score =  128 bits (323), Expect = 1e-36
 Identities = 34/97 (35%), Positives = 55/97 (56%), Gaps = 1/97 (1%)

Query: 234 PKHATPKNR-PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
                P  R  +   + +K+F+GG+S +T+ E ++ Y+ Q+GK+ + V++ D  +KR RG
Sbjct: 11  TLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70

Query: 293 FGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
           FGFVTF +   VD       H I  + VE K+A  +E
Sbjct: 71  FGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVARE 107

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

 Score =  142 bits (361), Expect = 2e-42
 Identities = 46/75 (61%), Positives = 57/75 (76%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 223 PIHTLDGKKIDPKHA 237
             H LD K IDPK A
Sbjct: 62  SRHELDSKTIDPKVA 76

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

 Score =  118 bits (298), Expect = 3e-33
 Identities = 32/75 (42%), Positives = 50/75 (66%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S  T+ E ++ YF QFG+V+E +++ D  TKR RGFGFVTF ++  VD +   
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 311 HFHMIKNKKVECKKA 325
             H + +K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

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

 Score =  142 bits (361), Expect = 2e-42
 Identities = 44/84 (52%), Positives = 55/84 (65%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
            + ++  + K+FVGGLSW TS + L++YF  FG V D  I  DP T RSRGFGFI F + 
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 214 ETVEKVLKVPIHTLDGKKIDPKHA 237
            +VEKVL    H LDG+ IDPK A
Sbjct: 64  ASVEKVLDQKEHRLDGRVIDPKKA 87

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

 Score =  120 bits (304), Expect = 5e-34
 Identities = 32/85 (37%), Positives = 52/85 (61%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           N  K      K+FVGG+S DTS +++K YF++FG+V +  + MD  T R RGFGF+ F++
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 301 EEVVDHICEIHFHMIKNKKVECKKA 325
              V+ + +   H +  + ++ KKA
Sbjct: 63  AASVEKVLDQKEHRLDGRVIDPKKA 87

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score =  143 bits (362), Expect = 2e-42
 Identities = 40/94 (42%), Positives = 62/94 (65%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           +    G+++ KIFVGG+  +    E++ YF +FG V E VM+ D + +R RGFGF+TFE+
Sbjct: 2   SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61

Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
           E+ VD    +HFH I  KKVE K+A+P+++  + 
Sbjct: 62  EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSG 95

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score =  135 bits (342), Expect = 2e-39
 Identities = 35/85 (41%), Positives = 53/85 (62%)

Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
                S K+FVGG+       +LREYF  FG VT+V+++ D   QR RGFGFITF + ++
Sbjct: 5   SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64

Query: 216 VEKVLKVPIHTLDGKKIDPKHATPK 240
           V++ + +  H + GKK++ K A P+
Sbjct: 65  VDQAVNMHFHDIMGKKVEVKRAEPR 89

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  147 bits (374), Expect = 3e-42
 Identities = 52/235 (22%), Positives = 79/235 (33%), Gaps = 21/235 (8%)

Query: 143 GKSSGDSGRSTPTGDDPTS-AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
           G +        P     T   +LFVG L    + E  +  F  +G  ++V I +D     
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDT 261
            RGFGFI        E         LDG  +  +      R +       + V  +S   
Sbjct: 58  -RGFGFIRLESRTLAEIA----KAELDGTILKSRPL----RIRFATHGAALTVKNLSPVV 108

Query: 262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-----IHFHMIK 316
           S E ++  FSQFG VE+ V+++D    R  G GFV F  +       E            
Sbjct: 109 SNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT 167

Query: 317 NKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQA 371
            + V  +  +  +          +        R   P    P T      S+ +A
Sbjct: 168 PRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKA 222

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  145 bits (367), Expect = 7e-42
 Identities = 27/192 (14%), Positives = 71/192 (36%), Gaps = 23/192 (11%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-----IMKDPITQRSRGFGFITFAEPET 215
           + +L+VG + +  + E + ++F     +  +       +      + + F F+ F   + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 216 VEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTK-----------------KIFVGGVS 258
             + +        G+ +  +           +                    K+F+GG+ 
Sbjct: 64  TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123

Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKN 317
              + ++VK   + FG ++   ++ D  T   +G+ F  + +  V D  I  ++   + +
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183

Query: 318 KKVECKKAQPKE 329
           KK+  ++A    
Sbjct: 184 KKLLVQRASVGA 195

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 89.3 bits (222), Expect = 4e-21
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 9/106 (8%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
           +   S        T    ++ KLF+GGL    + ++++E    FG +    ++KD  T  
Sbjct: 95  SENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL 154

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDG-----KKIDPKHATPKNR 242
           S+G+ F  + +    ++     I  L+G     KK+  + A+   +
Sbjct: 155 SKGYAFCEYVDINVTDQA----IAGLNGMQLGDKKLLVQRASVGAK 196

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 68.1 bits (167), Expect = 1e-13
 Identities = 9/94 (9%), Positives = 36/94 (38%), Gaps = 5/94 (5%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFEN 300
           G   ++++VG +    + E +  +F+   ++          ++  Q  + + F F+ F +
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
            +           + + + ++ ++    + +   
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGM 94

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  140 bits (356), Expect = 1e-40
 Identities = 34/173 (19%), Positives = 70/173 (40%), Gaps = 15/173 (8%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           +  L V  L    +  +L   F   G +    IM+D  T  S G+ F+ F      ++ +
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 221 KVPIHTLDGKKIDPK-----HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK 275
           K     L+G  +  K     +A P            ++V  + +  + +++   F ++G 
Sbjct: 63  K----VLNGITVRNKRLKVSYARPGGESIKDT---NLYVTNLPRTITDDQLDTIFGKYGS 115

Query: 276 VEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIK--NKKVECKKA 325
           + +  +L D+ T R RG  FV +   E     I  ++  + +  ++ +  + A
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 87.6 bits (218), Expect = 9e-21
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
             + P G+      L+V  L    + ++L   FG +G++    I++D +T R RG  F+ 
Sbjct: 78  SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137

Query: 210 FAEPETVEKVLKVPIHTLDGKKID 233
           + + E  ++     I  L+    +
Sbjct: 138 YNKREEAQEA----ISALNNVIPE 157

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

 Score =  136 bits (344), Expect = 4e-40
 Identities = 34/75 (45%), Positives = 48/75 (64%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T+ E ++ YF  FG V D ++M D  T R RGFGF+TF   + VEKV ++
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 223 PIHTLDGKKIDPKHA 237
             H ++ K ++ K A
Sbjct: 61  HFHEINNKMVECKKA 75

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

 Score =  131 bits (333), Expect = 2e-38
 Identities = 48/75 (64%), Positives = 63/75 (84%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S +T+ E+VK YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEI
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 311 HFHMIKNKKVECKKA 325
           HFH I NK VECKKA
Sbjct: 61  HFHEINNKMVECKKA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score =  133 bits (336), Expect = 7e-39
 Identities = 35/75 (46%), Positives = 46/75 (61%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T  EK+REYFG FG V  + +  D  T + RGF FITF E E V+K+++ 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 223 PIHTLDGKKIDPKHA 237
             H +   K + K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score =  132 bits (334), Expect = 1e-38
 Identities = 35/75 (46%), Positives = 47/75 (62%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S DT  E+++ YF  FG+VE   + MD +T + RGF F+TF+ EE V  I E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 311 HFHMIKNKKVECKKA 325
            +H +   K E K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  132 bits (334), Expect = 7e-37
 Identities = 46/197 (23%), Positives = 85/197 (43%), Gaps = 17/197 (8%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G  G   P+      A L+VG L    +   L E F   G +  + + +D IT+RS G+ 
Sbjct: 1   GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-------HATPKNRPKIGNRTKKIFVGGVSQ 259
           ++ F +P   E+ L     T++   I  K          P  R         IF+  + +
Sbjct: 61  YVNFQQPADAERALD----TMNFDVIKGKPVRIMWSQRDPSLRKSGVGN---IFIKNLDK 113

Query: 260 DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNK 318
               + +   FS FG +    ++ D      +G+GFV FE +E  +  I +++  ++ ++
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171

Query: 319 KVECKKAQPKEAVQANL 335
           KV   + + ++  +A L
Sbjct: 172 KVFVGRFKSRKEREAEL 188

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  130 bits (330), Expect = 2e-35
 Identities = 24/182 (13%), Positives = 58/182 (31%), Gaps = 13/182 (7%)

Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           +     +     + V  L    +  K+ +YF   G +  V +      +++  F  I FA
Sbjct: 32  NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFA 89

Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFS 271
             +     +      +   +I   H T             +++       +   ++    
Sbjct: 90  RYDGALAAITKTHKVVGQNEIIVSHLTECT----------LWMTNFPPSYTQRNIRDLLQ 139

Query: 272 QFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI-HFHMIKNKKVECKKAQPKEA 330
               V  ++ L   +    R F ++   ++E   +  E  +   I+   +  K + P E 
Sbjct: 140 DINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK 199

Query: 331 VQ 332
            +
Sbjct: 200 SK 201

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  128 bits (324), Expect = 1e-34
 Identities = 27/177 (15%), Positives = 69/177 (38%), Gaps = 9/177 (5%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           T   L++       +   +R+       V   + +       SR F +I     E     
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 220 LKVPIH--TLDGKKIDPKHATPKNRPKIGNRTK----KIFVGGVSQDTSAEE-VKAYFSQ 272
           ++  ++   ++G  +  K + P  + K  +       +I +  +S +   E  ++  F  
Sbjct: 176 VEK-LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG 234

Query: 273 FGKVEET-VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK 328
           FG +E+  +    ++   +    F+ FEN++  +   +++  ++ N+++    A  K
Sbjct: 235 FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 71.2 bits (175), Expect = 5e-14
 Identities = 13/137 (9%), Positives = 33/137 (24%), Gaps = 14/137 (10%)

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDT 261
           S  +G     +        K P+                           + V  + +  
Sbjct: 1   SMEYGHHARPDS-------KRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSY 53

Query: 262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVE 321
           +  +V  YF   G +    +      K++  F  + F   +           ++   ++ 
Sbjct: 54  NQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKTHKVVGQNEII 111

Query: 322 CKKAQPKEAVQANLLVG 338
                     +  L + 
Sbjct: 112 VSHLT-----ECTLWMT 123

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score =  120 bits (303), Expect = 6e-34
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
                +K+FVG  +   ++E+L+++F  +G V DV I K       R F F+TFA+ +  
Sbjct: 7   HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVA 61

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKN 241
           + +       + G  +   +A PK+
Sbjct: 62  QSLCGED-LIIKGISVHISNAEPKH 85

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score =  120 bits (302), Expect = 8e-34
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 6/90 (6%)

Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           +      +   K+FVG  ++D +AEE++ +F Q+G+V +  +      K  R F FVTF 
Sbjct: 2   RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFA 56

Query: 300 NEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
           +++V   +C     +IK   V    A+PK 
Sbjct: 57  DDKVAQSLCGED-LIIKGISVHISNAEPKH 85

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score =  119 bits (301), Expect = 1e-33
 Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
              S+ +FVG  +   + ++LRE+F  +G V DV I K       R F F+TFA+ +  +
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQ 56

Query: 218 KVLKVPIHTLDGKKIDPKHATPKN 241
            +       + G  +   +A PK+
Sbjct: 57  SLCGED-LIIKGISVHISNAEPKH 79

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score =  118 bits (299), Expect = 2e-33
 Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           + +  +FVG  + D + +E++ +FSQ+G V +  +      K  R F FVTF ++++   
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQS 57

Query: 307 ICEIHFHMIKNKKVECKKAQPKE 329
           +C     +IK   V    A+PK 
Sbjct: 58  LCGED-LIIKGISVHISNAEPKH 79

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score =  121 bits (306), Expect = 2e-33
 Identities = 36/169 (21%), Positives = 76/169 (44%), Gaps = 12/169 (7%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L+VG L    + + L++YF + G + ++ IM D    ++  + F+ + +       L+  
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ-- 59

Query: 224 IHTLDGKKIDPKH-----ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
             TL+GK+I+        A    +    + T  +FVG ++ +   E ++  F  F     
Sbjct: 60  --TLNGKQIENNIVKINWAFQSQQSSSDD-TFNLFVGDLNVNVDDETLRNAFKDFPSYLS 116

Query: 279 TVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQ 326
             ++ D QT   RG+GFV+F +++   + +  +    +  + +    A 
Sbjct: 117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 76.4 bits (189), Expect = 7e-17
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
           +N  +               +  LFVG L+     E LR  F  F +     +M D  T 
Sbjct: 73  IN-WAFQS-----QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG 126

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
            SRG+GF++F   +  +      + ++ G+ ++
Sbjct: 127 SSRGYGFVSFTSQDDAQNA----MDSMQGQDLN 155

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 66.0 bits (162), Expect = 4e-13
 Identities = 17/94 (18%), Positives = 39/94 (41%), Gaps = 6/94 (6%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           + ++VG + +  + + +K YF   G +    +++D +  ++  + FV +      +   +
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59

Query: 310 I-HFHMIKNKKVECKKAQPK----EAVQANLLVG 338
             +   I+N  V+   A            NL VG
Sbjct: 60  TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVG 93

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score =  110 bits (277), Expect = 5e-30
 Identities = 34/101 (33%), Positives = 57/101 (56%), Gaps = 1/101 (0%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G S  +G      KLFVGGLS+ T+ + L + F  +G +++V+++KD  TQRSRGFGF+T
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 210 FAEPETVEKVLKVPI-HTLDGKKIDPKHATPKNRPKIGNRT 249
           F   +  +  +      ++DG++I    A   +  + G  +
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 90.4 bits (225), Expect = 2e-22
 Identities = 27/82 (32%), Positives = 51/82 (62%), Gaps = 1/82 (1%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
             K+FVGG+S DT+ + ++  FS++G++ E V++ D++T+R RGFGFVTFEN +     +
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
             ++   +  +++   +A    
Sbjct: 72  MAMNGKSVDGRQIRVDQAGKSS 93

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score =  108 bits (273), Expect = 2e-29
 Identities = 28/103 (27%), Positives = 50/103 (48%), Gaps = 4/103 (3%)

Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           S P G       +FVGG+  +    ++R +F  +G+V +V I+ D  T  S+G+GF++F 
Sbjct: 1   SLPEGK-IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 58

Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHATPK-NRPKIGNRTKKIF 253
               V+K+++       GKK+    A  K N      + + + 
Sbjct: 59  NDVDVQKIVESQ-INFHGKKLKLGPAIRKQNLSTYHVQPRPLI 100

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score =  108 bits (273), Expect = 2e-29
 Identities = 25/94 (26%), Positives = 48/94 (51%), Gaps = 2/94 (2%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           + P+       +FVGG+       E++++F+++G V+E  ++ D +T   +G+GFV+F N
Sbjct: 1   SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 59

Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
           +  V  I E        KK++   A  K+ +   
Sbjct: 60  DVDVQKIVE-SQINFHGKKLKLGPAIRKQNLSTY 92

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score =  106 bits (266), Expect = 3e-28
 Identities = 33/93 (35%), Positives = 50/93 (53%), Gaps = 2/93 (2%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +     KLF+GGL+ +T+ + L+  FG  G +++VL++KD  T +SRGF FITF  P   
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61

Query: 217 EKVLKVPI-HTLDGKKIDPKHATPKNRPKIGNR 248
           +   K     +L GK I  + A   +    G R
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 84.7 bits (210), Expect = 3e-20
 Identities = 22/85 (25%), Positives = 50/85 (58%), Gaps = 2/85 (2%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
            +   K+F+GG++++T+ + +KA F + G + E +++ D +T + RGF F+TFEN     
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62

Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
           +   +++   +  K ++ ++A+   
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPS 87

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score =  104 bits (261), Expect = 1e-27
 Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 7/103 (6%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    D      +F+  LS+ +  E L E    FG +  V ++  P T+ S+G  
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 207 FITFAEPETVEKVLK-------VPIHTLDGKKIDPKHATPKNR 242
           F  F   E  +K L             LDG+++    A  ++ 
Sbjct: 61  FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 83.2 bits (206), Expect = 9e-20
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 7/98 (7%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
               P      K +F+  +S D+  E +     QFG ++   +++   T+  +G  F  F
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 299 ENEEVVD-------HICEIHFHMIKNKKVECKKAQPKE 329
             +E             E     +  ++++   A  ++
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 102

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

 Score =  103 bits (259), Expect = 1e-27
 Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            +FV G      S +L EYF  FG V  V++ KD        F  +   +    E VL  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGAREAVLSQ 64

Query: 223 PIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
             H+L G ++  +    K      +++ K
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPASKSPK 93

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

 Score =  100 bits (252), Expect = 2e-26
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 5/84 (5%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
            +  + +FV G  +   + ++  YF  FG V   V++     K    F  V   +    +
Sbjct: 5   SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVAS-VVMD----KDKGVFAIVEMGDVGARE 59

Query: 306 HICEIHFHMIKNKKVECKKAQPKE 329
            +     H +   ++  +  + KE
Sbjct: 60  AVLSQSQHSLGGHRLRVRPREQKE 83

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score =  100 bits (251), Expect = 2e-26
 Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 4/87 (4%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    +   +  L V GLS  T+   LRE F  +G + DV I+ D  ++RSRGF 
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
           F+ F   +  ++         +G ++D
Sbjct: 61  FVYFENVDDAKEA----KERANGMELD 83

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 81.5 bits (202), Expect = 2e-19
 Identities = 19/66 (28%), Positives = 36/66 (54%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
           +         +    + V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV
Sbjct: 3   SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

Query: 297 TFENEE 302
            FEN +
Sbjct: 63  YFENVD 68

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score =  101 bits (253), Expect = 2e-26
 Identities = 25/102 (24%), Positives = 46/102 (45%), Gaps = 1/102 (0%)

Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
           GKS         + ++  +  +F   L+ +     L ++F   G V DV I+ D  ++RS
Sbjct: 7   GKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRS 66

Query: 203 RGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP-KNRP 243
           +G  ++ F E ++V   + +    L G  I  + +   KNR 
Sbjct: 67  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRL 108

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 93.5 bits (233), Expect = 1e-23
 Identities = 17/102 (16%), Positives = 43/102 (42%), Gaps = 2/102 (1%)

Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT 287
            GK    +     +  +   RT  +F   ++      +++ +FS  GKV +  ++ D+ +
Sbjct: 6   SGKSPVREPVDNLSPEERDART--VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63

Query: 288 KRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
           +R +G  +V F   + V     +    +    +  + +Q ++
Sbjct: 64  RRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK 105

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 99.2 bits (248), Expect = 7e-26
 Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P  D   +  L V  L+++TS + LR  F  +G V DV I ++P T+  RGF 
Sbjct: 1   GSSGSSGPDVDGMIT--LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
           F+ F +    +         +DG ++D
Sbjct: 59  FVRFHDRRDAQDA----EAAMDGAELD 81

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 77.7 bits (192), Expect = 7e-18
 Identities = 14/61 (22%), Positives = 28/61 (45%)

Query: 242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
                +    + V  ++  TS + ++  F ++G+V +  +  +  TK  RGF FV F + 
Sbjct: 6   SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDR 65

Query: 302 E 302
            
Sbjct: 66  R 66

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 96.5 bits (241), Expect = 9e-25
 Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G S  +G   T   L+VGGL+ +   + L   F  FG +TD+ I  D  T++ RGF F+ 
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
           F   E         I  ++  ++  +      A P    + G  
Sbjct: 61  FELAEDAAAA----IDNMNESELFGRTIRVNLAKPMRIKESGPS 100

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
              + ++VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E    
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 307 -ICEIHFHMIKNKKVECKKAQPKE 329
            I  ++   +  + +    A+P  
Sbjct: 70  AIDNMNESELFGRTIRVNLAKPMR 93

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 96.7 bits (241), Expect = 1e-24
 Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 11/108 (10%)

Query: 142 NGKSSGDSGRSTPTGDDP-TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
            G+  G   R      +P  +  L V GLS  T+   LRE F  +G + DV I+ D  ++
Sbjct: 26  GGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSR 85

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRP 243
           RSRGF F+ F   +  ++         +G ++D +      +  K RP
Sbjct: 86  RSRGFAFVYFENVDDAKEA----KERANGMELDGRRIRVDFSITK-RP 128

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 78.6 bits (194), Expect = 6e-18
 Identities = 19/69 (27%), Positives = 37/69 (53%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
            + +         +    + V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF
Sbjct: 31  GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90

Query: 294 GFVTFENEE 302
            FV FEN +
Sbjct: 91  AFVYFENVD 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 95.4 bits (238), Expect = 2e-24
 Identities = 31/107 (28%), Positives = 48/107 (44%), Gaps = 9/107 (8%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P  +    A ++VGGL  + S   L E F   G V +  + KD +T + +G+G
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
           F+ F   E  +  +K     +D  K+  K      A+  N+   G  
Sbjct: 61  FVEFLSEEDADYAIK----IMDMIKLYGKPIRVNKASAHNKNLSGPS 103

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 77.3 bits (191), Expect = 9e-18
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           N+   ++VGG+ +  S   +   F Q G V  T M  D+ T +H+G+GFV F +EE  D+
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72

Query: 307 ICEI-HFHMIKNKKVECKKAQPKE 329
             +I     +  K +   KA    
Sbjct: 73  AIKIMDMIKLYGKPIRVNKASAHN 96

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

 Score = 95.6 bits (238), Expect = 4e-24
 Identities = 31/113 (27%), Positives = 46/113 (40%), Gaps = 10/113 (8%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
                G      P  D      L V  L+++TS + LR  F  +G V DV I +D  T+ 
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
           SRGF F+ F +    E      +  +DG  +D +      A    RP   + +
Sbjct: 88  SRGFAFVRFHDKRDAEDA----MDAMDGAVLDGRELRVQMARYG-RPPDSHHS 135

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

 Score = 75.2 bits (185), Expect = 1e-16
 Identities = 17/74 (22%), Positives = 35/74 (47%)

Query: 229 GKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTK 288
           G+++     +    P        + V  ++  TS + ++  F ++G+V +  +  D+ TK
Sbjct: 27  GQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 86

Query: 289 RHRGFGFVTFENEE 302
             RGF FV F ++ 
Sbjct: 87  ESRGFAFVRFHDKR 100

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 94.2 bits (235), Expect = 5e-24
 Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 6/89 (6%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG S   G  P+ + ++V  L +  ++  L   F  +G V  V IMKD  T++S+G
Sbjct: 2   SSGSSGMSG--GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
             FI F + ++ +         ++ K++ 
Sbjct: 60  VAFILFLDKDSAQNC----TRAINNKQLF 84

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 73.8 bits (182), Expect = 1e-16
 Identities = 11/53 (20%), Positives = 30/53 (56%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             ++V  +    +  ++   FS++GKV +  ++ D+ T++ +G  F+ F +++
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69

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

 Score = 95.6 bits (238), Expect = 6e-24
 Identities = 25/89 (28%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
             G  G     G   T   L+VGGL+ +   + L   F  FG +TD+ I  D  T++ RG
Sbjct: 47  DGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 106

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
           F F+ F   E         I  ++  ++ 
Sbjct: 107 FAFVEFELAEDAAAA----IDNMNESELF 131

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

 Score = 80.6 bits (199), Expect = 1e-18
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 6/95 (6%)

Query: 214 ETVEKVLKVPIHT------LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK 267
           E  E +  +P            + +D                + ++VGG++++   + + 
Sbjct: 22  EMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLH 81

Query: 268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           A F  FG + +  + +D +T++HRGF FV FE  E
Sbjct: 82  AAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 93.8 bits (234), Expect = 9e-24
 Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 4/87 (4%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P      +A + V  LS  T    L+E F  FG+++ + + KD  T +S+GF 
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
           FI+F   E   +     I  + G   D
Sbjct: 61  FISFHRREDAARA----IAGVSGFGYD 83

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 74.6 bits (184), Expect = 9e-17
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 1/88 (1%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            +  +    I V  +S+DT   +++  F  FG +    +  D+ T + +GF F++F   E
Sbjct: 9   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68

Query: 303 VVDH-ICEIHFHMIKNKKVECKKAQPKE 329
                I  +      +  +  + A+P  
Sbjct: 69  DAARAIAGVSGFGYDHLILNVEWAKPST 96

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 93.9 bits (234), Expect = 9e-24
 Identities = 29/101 (28%), Positives = 51/101 (50%), Gaps = 3/101 (2%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S  +    T  +L V  + ++     LR+ FG FG + DV I+ +   + S+GFG
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFG 58

Query: 207 FITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPKIG 246
           F+TF      ++  + +    ++G+KI+  +AT +     G
Sbjct: 59  FVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
                +  +  K++ V  +       +++  F QFGK+ +  ++ +++    +GFGFVTF
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTF 62

Query: 299 ENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
           EN    D    ++H  +++ +K+E   A  + 
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARV 94

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

 Score = 95.4 bits (237), Expect = 9e-24
 Identities = 30/141 (21%), Positives = 62/141 (43%), Gaps = 3/141 (2%)

Query: 114 PTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQT 173
            +G D  +  L+   +       Q       +   +   T +G     A ++VG  SW T
Sbjct: 8   SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWT 67

Query: 174 SSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KVPIHTLDGK 230
           + ++L +     G   V ++   ++    +S+G+  +  A   +V K+L  +P   L+G+
Sbjct: 68  TDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE 127

Query: 231 KIDPKHATPKNRPKIGNRTKK 251
           K+D + AT +N  +   + +K
Sbjct: 128 KVDVRPATRQNLSQFEAQARK 148

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

 Score = 66.5 bits (162), Expect = 2e-13
 Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 3/107 (2%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFG 294
           A       + NR   ++VG  S  T+ +++       G   V E     ++   + +G+ 
Sbjct: 43  AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA 102

Query: 295 FVTFENEEVVDHICE-IHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
            V   +E  V  + E +   ++  +KV+ + A  +   Q      KR
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 93.5 bits (233), Expect = 1e-23
 Identities = 28/106 (26%), Positives = 45/106 (42%), Gaps = 14/106 (13%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S     D  + KLF+G +      + L+  F  FG + ++ ++KD  T   +G  
Sbjct: 1   GSSGSSGMK--DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCA 58

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDP--------KHATPKNRPK 244
           F+T+ E E+  K        L  +K  P        K A  ++R  
Sbjct: 59  FLTYCERESALKA----QSALHEQKTLPGMNRPIQVKPADSESRGG 100

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 80.4 bits (199), Expect = 7e-19
 Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
            K+F+G + ++   +++K  F +FGK+ E  +L D+ T  H+G  F+T+   E       
Sbjct: 14  IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73

Query: 309 EIHFHMI---KNKKVECKKAQPKEAVQA 333
            +H        N+ ++ K A  +    +
Sbjct: 74  ALHEQKTLPGMNRPIQVKPADSESRGGS 101

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

 Score = 93.5 bits (232), Expect = 1e-23
 Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 9/96 (9%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH--RGFGFVTFENEEVVD 305
            ++K+FVGG+  D   +E+ A F +FG +        +       +G+ F+ F+ E  V 
Sbjct: 7   GSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66

Query: 306 -------HICEIHFHMIKNKKVECKKAQPKEAVQAN 334
                        +  + +  ++ K  Q +    ++
Sbjct: 67  ALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSD 102

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

 Score = 84.6 bits (209), Expect = 3e-20
 Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 9/95 (9%)

Query: 155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKD--PITQRSRGFGFITFAE 212
           +     S K+FVGGL      +++   F  FG +      K         +G+ F+ F E
Sbjct: 2   SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 213 PETVEKVLKVPIH-------TLDGKKIDPKHATPK 240
             +V+ ++   +         +    I  K    +
Sbjct: 62  ESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIR 96

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 92.7 bits (230), Expect = 2e-23
 Identities = 27/116 (23%), Positives = 39/116 (33%), Gaps = 20/116 (17%)

Query: 155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMF-----GAVTDVLIMKDPITQRSRGFGFIT 209
           +        + V GL      E L  YF        G V           QR    G +T
Sbjct: 2   SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLT 53

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEE 265
           F EP   E+VL    H L G ++  + A P+          ++ + G+   TS   
Sbjct: 54  FREPADAERVLAQADHELHGAQLSLRPAPPRA-------PARLLLQGLPPGTSGPS 102

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 65.4 bits (159), Expect = 1e-13
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 13/86 (15%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYF-----SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
              + V G+      E +  YF     S  G V           +R    G +TF     
Sbjct: 8   GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFREPAD 59

Query: 304 VDHICEIHFHMIKNKKVECKKAQPKE 329
            + +     H +   ++  + A P+ 
Sbjct: 60  AERVLAQADHELHGAQLSLRPAPPRA 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 91.8 bits (229), Expect = 3e-23
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
            T   L+VGGL+ +   + L   F  FG +TD+ I  D  T++ RGF F+ F   E    
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 219 VLKVPIHTLDGKKID 233
                I  ++  ++ 
Sbjct: 65  A----IDNMNESELF 75

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 80.3 bits (199), Expect = 4e-19
 Identities = 18/56 (32%), Positives = 34/56 (60%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
              + ++VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

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

 Score = 92.0 bits (229), Expect = 3e-23
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPE 214
                  + +  ++  T  + +      + +  V ++ ++KD  TQ++RGF F+  +   
Sbjct: 6   HHHMD-TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 215 TVEKVLKV-----PIHTLDGKKI 232
              ++L++     P   +DGK I
Sbjct: 65  DASQLLQILQSLHPPLKIDGKTI 87

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

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGK--VEETVMLMDQQTKRHRGFGFVTFENEE 302
              I +  ++  T  + +    S +    V    ++ D+QT+++RGF FV   +  
Sbjct: 9   MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 91.0 bits (227), Expect = 4e-23
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           +  LFVG L+     E LR  F  F +     +M D  T  SRG+GF++F   +  +   
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA- 59

Query: 221 KVPIHTLDGKKIDPK-----HATPK 240
              + ++ G+ ++ +      A   
Sbjct: 60  ---MDSMQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 76.4 bits (189), Expect = 9e-18
 Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
           T  +FVG ++ +   E ++  F  F       ++ D QT   RG+GFV+F +++   + +
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
             +    +  + +    A   E
Sbjct: 61  DSMQGQDLNGRPLRINWAAKLE 82

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 91.1 bits (227), Expect = 7e-23
 Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 14/100 (14%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
               S +LFV  LS+ +S E L + F  +G ++++    D +T++ +GF F+TF  PE  
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 217 EKVLKVPIHTLDGKKID----------PKHATPKNRPKIG 246
            K        +DG+              K    ++ P  G
Sbjct: 64  VKA----YAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 74.2 bits (183), Expect = 9e-17
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
               + + ++FV  +S  +S E+++  FS +G + E    +D  TK+ +GF FVTF   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 90.8 bits (226), Expect = 1e-22
 Identities = 33/108 (30%), Positives = 43/108 (39%), Gaps = 12/108 (11%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S P      S  LFV GLS  T+ E L+E    F       I+ D  T  S+GFG
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFG 57

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
           F+ F   E  +         ++  +ID        A PK     G  +
Sbjct: 58  FVDFNSEEDAKAA----KEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
           +K +FV G+S+DT+ E +K  F    +     ++ D++T   +GFGFV F +EE      
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
             +    I   KV    A+PK 
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKG 93

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 89.9 bits (224), Expect = 1e-22
 Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 9/90 (10%)

Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           G   +   +FVG LS + ++  +   F  FG ++D  ++KD  T +S+G+GF++F     
Sbjct: 1   GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 216 VEKVLKVPIHTLDGKKIDPK-----HATPK 240
            E      I  + G+ +  +      AT K
Sbjct: 61  AENA----IQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 72.6 bits (179), Expect = 2e-16
 Identities = 19/79 (24%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
            +FVG +S + +   + A F+ FG++ +  ++ D  T + +G+GFV+F N+   ++ I +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 310 IHFHMIKNKKVECKKAQPK 328
           +    +  +++    A  K
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 90.4 bits (225), Expect = 2e-22
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 1/93 (1%)

Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
                +  T   LF+G L+   S  +L+       A  D+ ++    T  +R FG++ F 
Sbjct: 8   PVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFE 66

Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHATPKNRPK 244
             E +EK L++    + G +I  +    ++  +
Sbjct: 67  SAEDLEKALELTGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 17/83 (20%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            +F+G ++ + S  E+K   S+     + + ++D +T  +R FG+V FE+ E ++   E+
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALEL 77

Query: 311 HFHMIKNKKVECKKAQPKEAVQA 333
               +   +++ +K + ++  + 
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTRG 100

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 90.5 bits (225), Expect = 2e-22
 Identities = 29/103 (28%), Positives = 48/103 (46%), Gaps = 9/103 (8%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    D      +FVG LS + ++E ++  F  FG ++D  ++KD  T +S+G+G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPK 244
           F++F      E      I  + G+ +  +      AT K    
Sbjct: 61  FVSFFNKWDAENA----IQQMGGQWLGGRQIRTNWATRKPPAP 99

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 72.0 bits (177), Expect = 9e-16
 Identities = 22/99 (22%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
           +    + K  +    +FVG +S + + E++KA F+ FG++ +  ++ D  T + +G+GFV
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62

Query: 297 TFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQAN 334
           +F N+   ++ I ++    +  +++    A  K     +
Sbjct: 63  SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 91.8 bits (228), Expect = 2e-22
 Identities = 30/113 (26%), Positives = 46/113 (40%), Gaps = 10/113 (8%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
               +  S       D      L V  L+++TS + LR  F  +G V DV I +D  T+ 
Sbjct: 51  TFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 110

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
           SRGF F+ F +    E      +  +DG  +D +      A    RP   + +
Sbjct: 111 SRGFAFVRFHDKRDAEDA----MDAMDGAVLDGRELRVQMARYG-RPPDSHHS 158

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 76.4 bits (188), Expect = 6e-17
 Identities = 20/116 (17%), Positives = 41/116 (35%), Gaps = 16/116 (13%)

Query: 203 RGFGFITFAEPETVEKVLKVPI-------HTLDGKKI----DPKHATPKNRPKIGNR--- 248
            G         E V+      +       + +DG+             +      +    
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 249 --TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
                + V  ++  TS + ++  F ++G+V +  +  D+ TK  RGF FV F ++ 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 89.2 bits (222), Expect = 4e-22
 Identities = 29/93 (31%), Positives = 48/93 (51%), Gaps = 4/93 (4%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ---RSRGFGFITFAEPETVE 217
           S+ LF+  L++ T+ E L+  F   GA+    I K         S GFGF+ + +PE  +
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 218 KVLK-VPIHTLDGKKIDPKHATPKNRPKIGNRT 249
           K LK +  HT+DG K++ + +    +P  G  +
Sbjct: 65  KALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 16/85 (18%), Positives = 38/85 (44%), Gaps = 4/85 (4%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTK---RHRGFGFVTFENEEVVD 305
           +  +F+  ++  T+ E +K  FS+ G ++   +   +         GFGFV ++  E   
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
             + ++  H +   K+E + ++   
Sbjct: 65  KALKQLQGHTVDGHKLEVRISERAT 89

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 87.7 bits (218), Expect = 1e-21
 Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 3/103 (2%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGF 205
           G SG S       T++K+ V  + +Q +  ++RE F  FG +  V + K    T   RGF
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 206 GFITFAEPETVEKVLKVPIH--TLDGKKIDPKHATPKNRPKIG 246
           GF+ F   +  +K      H   L G+++  + A  +   + G
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 70.4 bits (173), Expect = 3e-15
 Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGF 293
              +    PK    T KI V  +    +  E++  FS FG+++   +      T  HRGF
Sbjct: 2   SSGSSGQVPK-KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 294 GFVTFENEEVVDHICEIHFHM--IKNKKVECKKAQPKEAVQA 333
           GFV F  ++          H   +  +++  + A  +  VQ+
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 87.2 bits (217), Expect = 2e-21
 Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
             S+ L+VG L +  + + LR  F  FG + ++++MKD  T RS+G+GFITF++ E   +
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 219 VLKVPIHTLDGKKID 233
                +  L+G ++ 
Sbjct: 63  A----LEQLNGFELA 73

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 73.7 bits (182), Expect = 1e-16
 Identities = 16/54 (29%), Positives = 33/54 (61%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +  ++VG +  + + + ++  F  FGK++  V++ D  T R +G+GF+TF + E
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 86.9 bits (216), Expect = 3e-21
 Identities = 18/96 (18%), Positives = 44/96 (45%), Gaps = 9/96 (9%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S  +++G + +  + E++ +     G V ++ +M DP T RS+G+ FI F + E+     
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA- 60

Query: 221 KVPIHTLDGKKIDPK-----HATPKNRPKIGNRTKK 251
              +  L+G ++  +     +++  +   +      
Sbjct: 61  ---VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHH 93

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 74.6 bits (184), Expect = 6e-17
 Identities = 15/54 (27%), Positives = 29/54 (53%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           ++ +++G +  D + E++    S  G V    M+ D QT R +G+ F+ F + E
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 55

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 85.4 bits (212), Expect = 7e-21
 Identities = 29/89 (32%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG       +     +FVG L  +   E L E F   G +T V I KD    + + 
Sbjct: 2   SSGSSGM--FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKS 58

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
           FGF+ F  PE+V       I  L+G ++ 
Sbjct: 59  FGFVCFKHPESVSYA----IALLNGIRLY 83

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 65.7 bits (161), Expect = 9e-14
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
            +    P      + +FVG +      E +   F Q G + +  +  D++  + + FGFV
Sbjct: 4   GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFV 62

Query: 297 TFENEE 302
            F++ E
Sbjct: 63  CFKHPE 68

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 84.9 bits (211), Expect = 8e-21
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
              S+ L++ GL   T+ + L +    +G +     + D  T + +G+GF+ F  P   +
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 218 KVLKVPIHTLDGKKID 233
           K     +  L    + 
Sbjct: 62  KA----VTALKASGVQ 73

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 72.2 bits (178), Expect = 3e-16
 Identities = 12/54 (22%), Positives = 31/54 (57%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +  +++ G+   T+ +++      +GK+  T  ++D+ T + +G+GFV F++  
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 85.4 bits (212), Expect = 8e-21
 Identities = 24/107 (22%), Positives = 43/107 (40%), Gaps = 13/107 (12%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S  +     S  L +  LS+  + E L+E F     +     +      +S+G+ 
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYA 56

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
           FI FA  E  ++ L     + + ++I+ +        P+  P  G  
Sbjct: 57  FIEFASFEDAKEALN----SCNKREIEGRAIRLELQGPRGSPNSGPS 99

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 66.1 bits (162), Expect = 6e-14
 Identities = 9/53 (16%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K + +  +S   + E ++  F +   ++    +   Q  + +G+ F+ F + E
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFE 64

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 84.5 bits (210), Expect = 1e-20
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI-TQRSRGFGFITFAEPETVE 217
               K+ +G L+   + + + E F  +G +  + +  + +    S+G+ ++ F  P+  E
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61

Query: 218 KVLKVPIHTLDGKKID 233
           K LK     +DG +ID
Sbjct: 62  KALK----HMDGGQID 73

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 68.3 bits (168), Expect = 9e-15
 Identities = 12/56 (21%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD-QQTKRHRGFGFVTFENEE 302
           +  K+ +G ++++ + + +   FS +GK++   M ++       +G+ +V FEN +
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPD 58

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 84.5 bits (210), Expect = 1e-20
 Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 1/88 (1%)

Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           G +  +  ++VG + +  ++E+L  +F   G+V  V I+ D  +   +GF +I F++ E+
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 216 VEKVLKVPIHTLDGKKIDPKHATPKNRP 243
           V   L +      G++I        NRP
Sbjct: 61  VRTSLALDESLFRGRQIKVIPKRT-NRP 87

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 77.2 bits (191), Expect = 5e-18
 Identities = 18/81 (22%), Positives = 40/81 (49%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
            + I+VG V    +AEE++A+F   G V    +L D+ +   +GF ++ F ++E V    
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
            +   + + ++++    +   
Sbjct: 66  ALDESLFRGRQIKVIPKRTNR 86

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 86.4 bits (214), Expect = 2e-20
 Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
                     S  L+VG LS+ T+ E++ E F   G +  +++  D + + + GF F+ +
Sbjct: 29  NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88

Query: 211 AEPETVEKVLKVPIHTLDGKKID 233
                 E  ++     ++G ++D
Sbjct: 89  YSRADAENAMR----YINGTRLD 107

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 76.8 bits (189), Expect = 5e-17
 Identities = 20/114 (17%), Positives = 52/114 (45%), Gaps = 2/114 (1%)

Query: 218 KVLKVPIHTLDGKKIDPKH-ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV 276
           K L+   +    +  D       + + K+  ++  ++VG +S  T+ E++   FS+ G +
Sbjct: 7   KALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 277 EETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKE 329
           ++ +M +D+  K   GF FV + +  +  + +  I+   + ++ +        +
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK 120

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

 Score = 84.3 bits (209), Expect = 3e-20
 Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 7/100 (7%)

Query: 145 SSGDSGRSTPTGDDP--TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
           SSG   R +    +      +L V  + ++     LR+ FG FG + DV I+ +   + S
Sbjct: 11  SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGS 68

Query: 203 RGFGFITFAEPETVEKVLKVPIH--TLDGKKIDPKHATPK 240
           +GFGF+TF      ++  +  +H   ++G+KI+  +AT +
Sbjct: 69  KGFGFVTFENSADADRARE-KLHGTVVEGRKIEVNNATAR 107

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

 Score = 69.7 bits (171), Expect = 4e-15
 Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 5/96 (5%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
           P+ +      K     K++ V  +       +++  F QFGK+ +  ++ +++    +GF
Sbjct: 16  PRGSHMNTENKSQP--KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGF 71

Query: 294 GFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
           GFVTFEN    D    ++H  +++ +K+E   A  +
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

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

 Score = 83.5 bits (207), Expect = 4e-20
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 7/89 (7%)

Query: 147 GDSGRSTPTGD--DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           G SG S            KLF+ GL +  + E+L E     G V D+ ++ +    + +G
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
             ++ +       +     +  +DG  I 
Sbjct: 60  LAYVEYENESQASQA----VMKMDGMTIK 84

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

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
              R        K+F+ G+    + EE++      G V++  ++ + +  + +G  +V +
Sbjct: 7   GVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEY 65

Query: 299 ENEE 302
           ENE 
Sbjct: 66  ENES 69

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 83.5 bits (207), Expect = 5e-20
 Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 9/102 (8%)

Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
                +  +          +L+VG L +  + + LR  F  FG +  + +M D  T RS+
Sbjct: 9   SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPK 240
           G+GFITF++ E  +K     +  L+G ++  +     H T +
Sbjct: 69  GYGFITFSDSECAKKA----LEQLNGFELAGRPMKVGHVTER 106

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 72.3 bits (178), Expect = 5e-16
 Identities = 19/66 (28%), Positives = 37/66 (56%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
           A   N  K      +++VG +  + + + ++  F  FG++E   ++MD +T R +G+GF+
Sbjct: 14  AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73

Query: 297 TFENEE 302
           TF + E
Sbjct: 74  TFSDSE 79

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 84.0 bits (208), Expect = 6e-20
 Identities = 22/121 (18%), Positives = 46/121 (38%), Gaps = 16/121 (13%)

Query: 133 REAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL 192
           RE +  V  +G   G   RS           LFV G+  + + E + + F  +G + ++ 
Sbjct: 1   REDYDSVEQDGDEPGPQ-RSVE------GWILFVTGVHEEATEEDIHDKFAEYGEIKNIH 53

Query: 193 IMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGN 247
           +  D  T   +G+  + +   +  +      +  L+G+ +  +         +  PK   
Sbjct: 54  LNLDRRTGYLKGYTLVEYETYKEAQAA----MEGLNGQDLMGQPISVDWCFVRGPPKGKR 109

Query: 248 R 248
           R
Sbjct: 110 R 110

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 70.1 bits (172), Expect = 6e-15
 Identities = 12/52 (23%), Positives = 32/52 (61%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            +FV GV ++ + E++   F+++G+++   + +D++T   +G+  V +E  +
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 84.4 bits (209), Expect = 6e-20
 Identities = 28/132 (21%), Positives = 48/132 (36%), Gaps = 10/132 (7%)

Query: 125 FVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGM 184
            V   +   +  QL  +  +       +    +      L V  +       +LR+ F  
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFER 65

Query: 185 FGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATP 239
           +G +  V I+ D  T++SRG+GF+ F    + ++     I  L+G  I  K      A  
Sbjct: 66  YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA----IAGLNGFNILNKRLKVALAAS 121

Query: 240 K-NRPKIGNRTK 250
              RP I     
Sbjct: 122 GHQRPGIAGAVG 133

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 75.2 bits (185), Expect = 1e-16
 Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 1/97 (1%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
            +H  P       +  + + V  +       +++  F ++G +E   ++ D++T++ RG+
Sbjct: 27  QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86

Query: 294 GFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
           GFV F++       I  ++   I NK+++   A    
Sbjct: 87  GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 82.2 bits (204), Expect = 8e-20
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
            L++G L+W T+ E L E     G   + ++   ++    +S+GF  +      + +K++
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 221 -KVPIHTLDGKKIDPKHATPKN-RP 243
             +P   L G+      +       
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHHH 87

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 10/82 (12%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
            +++G ++  T+ E++       G   + E     ++   + +GF  V   +E      +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
             +    +  +      +   E
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLE 84

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 83.1 bits (206), Expect = 8e-20
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S         + +FV  L ++   +KL+E F M G V    I++D    +SRG G
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
            +TF +     +     I   +G+ + 
Sbjct: 60  TVTFEQSIEAVQA----ISMFNGQLLF 82

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV 304
           G     +FV  +      +++K  FS  G V    +L D +  + RG G VTFE   E V
Sbjct: 12  GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAV 70

Query: 305 DHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
             I   +  ++ ++ +  K  +            +    GP
Sbjct: 71  QAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGP 111

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 83.1 bits (206), Expect = 9e-20
 Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 9/105 (8%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
           +G +    G +    + P  A LF+  L  +   + L + F  FG V    +  D  T  
Sbjct: 6   SGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL 65

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKN 241
           S+ FGF+++  P + +      I +++G +I  K         KN
Sbjct: 66  SKCFGFVSYDNPVSAQAA----IQSMNGFQIGMKRLKVQLKRSKN 106

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
            +F+  + Q+   +++   F  FG V    + +D+QT   + FGFV+++N       I  
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLLVG 338
           ++   I  K+++ +  + K   ++    G
Sbjct: 87  MNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 82.7 bits (205), Expect = 1e-19
 Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S          KLFVG L+ Q S E +   F  FG + +  +++ P    S+G  
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATP 239
           F+ F+     +      IH L G +  P  ++ 
Sbjct: 60  FVKFSSHTEAQAA----IHALHGSQTMPGASSS 88

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 5/95 (5%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
                  G R +K+FVG +++  S E+V   F  FG ++E  +L        +G  FV F
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKF 63

Query: 299 EN-EEVVDHICEIHFHMI---KNKKVECKKAQPKE 329
            +  E    I  +H        +  +  K A   +
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK 98

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 19/93 (20%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
            D +   +FVG + ++ + E+L++ F   G V    ++ D  T + +G+GF  + + ET 
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 217 EKVLKVPIHTLDGKKIDPK-----HATPKNRPK 244
                  +  L+G++   +     +A  +   +
Sbjct: 64  LSA----MRNLNGREFSGRALRVDNAASEKNKE 92

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 16/60 (26%), Positives = 36/60 (60%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           P +    + +FVG +  + + E++K  FS+ G V    ++ D++T + +G+GF  ++++E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 81.2 bits (201), Expect = 4e-19
 Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 148 DSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGF 207
           DSG     G +    KL V  L +  S   ++E F  FG +    +  D  + RS G   
Sbjct: 17  DSGFGGGAGVET-GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTAD 74

Query: 208 ITFAEPETVEKVLKVPIHTLDGKKID 233
           + F       K +K      +G  +D
Sbjct: 75  VHFERKADALKAMK----QYNGVPLD 96

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 57.7 bits (140), Expect = 9e-11
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFG 294
              +            K+ V  +    S  +++  F++FG +++  +  D ++ R  G  
Sbjct: 15  LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTA 73

Query: 295 FVTFENEE 302
            V FE + 
Sbjct: 74  DVHFERKA 81

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 81.3 bits (201), Expect = 5e-19
 Identities = 19/107 (17%), Positives = 44/107 (41%), Gaps = 1/107 (0%)

Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
                   S     +     ++VG + + ++++ L  +F   G++  + I+ D  +   +
Sbjct: 19  TEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPK 78

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTK 250
           G+ +I FAE  +V+  + +      G+ I        N P I +  +
Sbjct: 79  GYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT-NMPGISSTDR 124

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 74.8 bits (184), Expect = 1e-16
 Identities = 14/81 (17%), Positives = 39/81 (48%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
            + ++VG V   ++A++++A+FS  G +    +L D+ +   +G+ ++ F     VD   
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
            +   + + + ++    +   
Sbjct: 96  AMDETVFRGRTIKVLPKRTNM 116

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 80.3 bits (199), Expect = 6e-19
 Identities = 30/107 (28%), Positives = 45/107 (42%), Gaps = 11/107 (10%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S           L+V  L      E+LR+ F  FG +T   +M +    RS+GFG
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
           F+ F+ PE   K     +  ++G+ +  K      A  K   + G  
Sbjct: 59  FVCFSSPEEATKA----VTEMNGRIVATKPLYVALAQRKEERQSGPS 101

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
            ++V  +      E ++  FS FG +    ++M+    R +GFGFV F + EE    + E
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74

Query: 310 IHFHMIKNKKVECKKAQPKE 329
           ++  ++  K +    AQ KE
Sbjct: 75  MNGRIVATKPLYVALAQRKE 94

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

 Score = 80.0 bits (198), Expect = 8e-19
 Identities = 20/117 (17%), Positives = 45/117 (38%), Gaps = 16/117 (13%)

Query: 132 VREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDV 191
           +RE +  V  +G   G   RS           LFV G+  + + E + + F  +G + ++
Sbjct: 1   MREDYDSVEQDGDEPGPQ-RSVE------GWILFVTGVHEEATEEDIHDKFAEYGEIKNI 53

Query: 192 LIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRP 243
            +  D  T   +G+  + +   +  +      +  L+G+ +  +         +  P
Sbjct: 54  HLNLDRRTGYLKGYTLVEYETYKEAQAA----MEGLNGQDLMGQPISVDWCFVRGPP 106

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

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 12/52 (23%), Positives = 32/52 (61%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            +FV GV ++ + E++   F+++G+++   + +D++T   +G+  V +E  +
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 79.2 bits (196), Expect = 2e-18
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    DD     L+VG LS   +   + + F   G      ++ +  +  +  + 
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYC 58

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
           F+ F E       L      ++G+KI 
Sbjct: 59  FVEFYEHRDAAAALA----AMNGRKIL 81

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
            + + ++VG +S+D +   +   FSQ G  +   M+ +  +  +  + FV F        
Sbjct: 13  GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAA 70

Query: 307 -ICEIHFHMIKNKKVECKKAQPKE 329
            +  ++   I  K+V+   A    
Sbjct: 71  ALAAMNGRKILGKEVKVNWATTPS 94

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 10/87 (11%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S         ++LFVG L    + E++R+ F  +G   +V I KD      +GFG
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
           FI        E         LD   + 
Sbjct: 55  FIRLETRTLAEIA----KVELDNMPLR 77

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 238 TPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
           +         R++ +FVG +  D + EE++  F ++GK  E  +       + +GFGF+ 
Sbjct: 5   SSGGEKTFTQRSR-LFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIR 57

Query: 298 FENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQA 333
            E   + +    E+    ++ K++  + A    ++ +
Sbjct: 58  LETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94

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

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            ++VG L +  +SE+++E F  FG V +V ++ D  T++ +GFGF+   E E+V +    
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEA--- 58

Query: 223 PIHTLDGKKID 233
            I  LD     
Sbjct: 59  -IAKLDNTDFM 68

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

 Score = 78.4 bits (194), Expect = 3e-18
 Identities = 27/80 (33%), Positives = 47/80 (58%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           + I+VG +    ++E+VK  FSQFGKV    ++ D++TK+ +GFGFV  + E V + I +
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 310 IHFHMIKNKKVECKKAQPKE 329
           +       + +   +A PK+
Sbjct: 62  LDNTDFMGRTIRVTEANPKK 81

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 79.7 bits (197), Expect = 2e-18
 Identities = 20/85 (23%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 149 SGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
                      T AKL V  L +  S   ++E F  FG +    +  D  + RS G   +
Sbjct: 23  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADV 81

Query: 209 TFAEPETVEKVLKVPIHTLDGKKID 233
            F       K +K       G  +D
Sbjct: 82  HFERRADALKAMK----QYKGVPLD 102

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 61.2 bits (149), Expect = 7e-12
 Identities = 14/106 (13%), Positives = 43/106 (40%), Gaps = 5/106 (4%)

Query: 234 PKHATPKNRPKIGNRTK---KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH 290
            +H    +    G   +   K+ V  +    S  +++  F++FG +++  +  D ++ R 
Sbjct: 17  WQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRS 75

Query: 291 RGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANL 335
            G   V FE   + +  + +     +  + ++ +    +  ++ + 
Sbjct: 76  LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 121

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

 Score = 79.4 bits (196), Expect = 2e-18
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 4/78 (5%)

Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           G      ++    L+       L++    +G V +V I+  P T++  G   + F     
Sbjct: 1   GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 216 VEKVLKVPIHTLDGKKID 233
            ++     +  L    + 
Sbjct: 61  AKET----VKNLHLTSVM 74

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

 Score = 70.9 bits (174), Expect = 2e-15
 Identities = 13/81 (16%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
           K++    ++ +     +K    ++G+VEE  +L+  +T++H G   V F +       + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
            +H   +    +  +     +
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQ 87

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 10/96 (10%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-IMKDPITQRSRGFGFITFAEPETVE 217
             S+ +F+G L  +   + L + F  FG +     IM+DP T  S+G+ FI FA  +  +
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 218 KVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
                 I  ++G+ +  +     +A  K+    G  
Sbjct: 63  AA----IEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM-DQQTKRHRGFGFVTFENEEVVDH-IC 308
            IF+G +  +   + +   FS FG + +T  +M D  T   +G+ F+ F + +  D  I 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
            ++   + N+ +    A  K+
Sbjct: 67  AMNGQYLCNRPITVSYAFKKD 87

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 78.5 bits (194), Expect = 2e-18
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAE 212
            +G    +A L++G L        +   F   G  V  V I+++ +T    G+ F+ FA+
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 213 PETVEKVLKVPIHTLDGKKID 233
             T EK     +H ++GK + 
Sbjct: 62  LATAEKC----LHKINGKPLP 78

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 10/75 (13%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
              +++G +        +   F+  G  V    ++ ++ T    G+ FV F +    +  
Sbjct: 9   AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68

Query: 307 ICEIHFHMIKNKKVE 321
           + +I+   +      
Sbjct: 69  LHKINGKPLPGATPA 83

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 78.9 bits (195), Expect = 3e-18
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 11/93 (11%)

Query: 145 SSGDSGRSTPTG----DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
           SSG SG S              +++VG L     ++ + + F  +GA+ D+ +       
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--- 58

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
               F F+ F +P   E      ++  DG   D
Sbjct: 59  GGPPFAFVEFEDPRDAEDA----VYGRDGYDYD 87

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.9 bits (156), Expect = 6e-13
 Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 3/64 (4%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
              R   GN   +I+VG +  D   ++++  F ++G + +  +      +    F FV F
Sbjct: 12  GVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEF 68

Query: 299 ENEE 302
           E+  
Sbjct: 69  EDPR 72

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

 Score = 80.7 bits (199), Expect = 3e-18
 Identities = 21/130 (16%), Positives = 37/130 (28%), Gaps = 5/130 (3%)

Query: 104 KSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAK 163
           ++     R      +  +               + +    +               T AK
Sbjct: 31  RNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAK 90

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L V  L +  S   ++E F  FG +    +  D  + RS G   + F       K +K  
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK-- 147

Query: 224 IHTLDGKKID 233
                G  +D
Sbjct: 148 --QYKGVPLD 155

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

 Score = 63.3 bits (154), Expect = 4e-12
 Identities = 14/110 (12%), Positives = 42/110 (38%), Gaps = 2/110 (1%)

Query: 227 LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ 286
           L  K       +     +      K+ V  +    S  +++  F++FG +++  +  D +
Sbjct: 66  LPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-R 124

Query: 287 TKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANL 335
           + R  G   V FE   + +  + +     +  + ++ +    +  ++ + 
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 174

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 78.1 bits (193), Expect = 3e-18
 Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
              +     +  L    LS+  + ++L+E F     +            +S+G  +I F 
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFK 61

Query: 212 EPETVEKVLKVPIHTLDGKKID 233
                EK L+       G +ID
Sbjct: 62  SEADAEKNLE----EKQGAEID 79

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 8/53 (15%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           + +    +S + + +E+K  F    ++      +  Q  + +G  ++ F++E 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEA 64

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

 Score = 78.5 bits (194), Expect = 4e-18
 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S            +VG L + T    +   F     +  V +++D  T + +GF 
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNR 248
           ++ F E +++++ L      L  + +    A  + + K G  
Sbjct: 60  YVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKSGPS 101

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

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 12/80 (15%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
              +VG +  +T   ++ A F     +    ++ D+ T + +GF +V F+  + +     
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 310 IHFHMIKNKKVECKKAQPKE 329
               ++ ++ +    A+ ++
Sbjct: 75  YDGALLGDRSLRVDIAEGRK 94

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

 Score = 77.7 bits (192), Expect = 7e-18
 Identities = 25/94 (26%), Positives = 37/94 (39%), Gaps = 10/94 (10%)

Query: 145 SSGDSGRSTP-----TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT 199
           SSG+  R  P        +P +  L++  LS + +   L   F  F       I    +T
Sbjct: 5   SSGEEIRKIPMFSSYNPGEP-NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT 63

Query: 200 QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
            R RG  FITF   E   + L      ++G K+ 
Sbjct: 64  GRMRGQAFITFPNKEIAWQALH----LVNGYKLY 93

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

 Score = 70.8 bits (174), Expect = 3e-15
 Identities = 16/86 (18%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           G   K +++  +S   +  ++ + F++F + +   +     T R RG  F+TF N+E+  
Sbjct: 22  GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81

Query: 306 H-ICEIHFHMIKNKKVECKKAQPKEA 330
             +  ++ + +  K +  +  + K+ 
Sbjct: 82  QALHLVNGYKLYGKILVIEFGKNKKQ 107

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 80.9 bits (199), Expect = 7e-18
 Identities = 18/114 (15%), Positives = 43/114 (37%), Gaps = 3/114 (2%)

Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPI 198
           V       +  +           L++G L+W T+ E L E     G   + ++   ++  
Sbjct: 48  VGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA 107

Query: 199 TQRSRGFGFITFAEPETVEKVL-KVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
             +S+GF  +      + +K++  +P   L G+         +   +   +++K
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 65.9 bits (160), Expect = 1e-12
 Identities = 17/130 (13%), Positives = 40/130 (30%), Gaps = 3/130 (2%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHR 291
            K A P        +   +++G ++  T+ E++       G   + E     ++   + +
Sbjct: 53  GKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK 112

Query: 292 GFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRM 350
           GF  V   +E      +  +    +  +         +   Q  +   K    G +    
Sbjct: 113 GFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172

Query: 351 AAPAPITPAT 360
            A  P   + 
Sbjct: 173 KAGPPGGSSR 182

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

 Score = 77.8 bits (192), Expect = 9e-18
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           + P    LF+  L  + +   L   F  FG V    +  D  T  S+ FGF++F  P++ 
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95

Query: 217 EKVLKVPIHTLDGKKIDPK 235
           +      I  ++G ++  K
Sbjct: 96  QVA----IKAMNGFQVGTK 110

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

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 20/101 (19%), Positives = 45/101 (44%), Gaps = 1/101 (0%)

Query: 227 LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ 286
           L    +    A    +   G     +F+  + Q+ +  ++ + F  FG V    + +D+Q
Sbjct: 18  LASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 77

Query: 287 TKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQ 326
           T   + FGFV+F+N +     I  ++   +  K+++ +  +
Sbjct: 78  TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 19/118 (16%), Positives = 42/118 (35%), Gaps = 16/118 (13%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
             S  +F+  L     ++ L + F  FG +    ++ D     S+G+GF+ F   E  E+
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60

Query: 219 VLKVPIHTLDGKKIDPK-----HATPKN-RPKIGNRTKK----IFVGGVSQDTSAEEV 266
                I  ++G  ++ +         +  R        K    +++      ++    
Sbjct: 61  A----IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAAA 114

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 66.5 bits (163), Expect = 9e-14
 Identities = 17/82 (20%), Positives = 41/82 (50%), Gaps = 3/82 (3%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
           +  IF+  + +    + +   FS FG +    ++ D      +G+GFV FE +E  +  I
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 62

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
            +++  ++ ++KV   + + ++
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRK 84

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 22/103 (21%), Positives = 40/103 (38%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S            F+G L +  + E ++E+F         L  +    +R +GFG
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
           +  F + +++   L +   +L  K+I    A        G  +
Sbjct: 61  YAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPSS 103

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 15/80 (18%), Positives = 33/80 (41%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
              F+G +  D + E +K +F         +       +R +GFG+  FE+ + +     
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 310 IHFHMIKNKKVECKKAQPKE 329
           ++   + NK++    A   +
Sbjct: 76  LNEESLGNKRIRVDVADQAQ 95

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 78.7 bits (194), Expect = 1e-17
 Identities = 16/115 (13%), Positives = 40/115 (34%), Gaps = 9/115 (7%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
             ++  D               LFV  +  +   ++++E F  +G + ++ +  D  T  
Sbjct: 53  RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 112

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRTKK 251
           S+G+  + +   +            L+G +I  +         K   ++    K+
Sbjct: 113 SKGYALVEYETHKQALAA----KEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 70.6 bits (173), Expect = 8e-15
 Identities = 10/54 (18%), Positives = 29/54 (53%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
              +FV  + ++   +E++  F  +G+++   + +D++T   +G+  V +E  +
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 76.2 bits (188), Expect = 2e-17
 Identities = 24/105 (22%), Positives = 38/105 (36%), Gaps = 15/105 (14%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S       +   L+V  L   TS E + + F          + K       R + 
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYA 54

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKH-----ATPKNRPKIG 246
           F+ F+  E   + +K     L+GK +D        A P ++   G
Sbjct: 55  FVHFSNREDAVEAMK----ALNGKVLDGSPIEVTLAKPVDKDSSG 95

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHI 307
            K ++V  +   TS E ++  F+             ++ K+ R + FV F N E+ V+ +
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVEAM 68

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
             ++  ++    +E   A+P +
Sbjct: 69  KALNGKVLDGSPIEVTLAKPVD 90

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

 Score = 76.6 bits (189), Expect = 2e-17
 Identities = 15/104 (14%), Positives = 36/104 (34%), Gaps = 11/104 (10%)

Query: 148 DSGRSTPTGDD--PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
           +       G         LFV  +  +   ++++E F  +G + ++ +  D  T  S+G+
Sbjct: 11  EDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY 70

Query: 206 GFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPK 244
             + +   +            L+G +I  +         K   +
Sbjct: 71  ALVEYETHKQALAA----KEALNGAEIMGQTIQVDWCFVKGPKR 110

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

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 11/64 (17%), Positives = 32/64 (50%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
            +  P+       +FV  + ++   +E++  F  +G+++   + +D++T   +G+  V +
Sbjct: 16  LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75

Query: 299 ENEE 302
           E  +
Sbjct: 76  ETHK 79

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 76.2 bits (188), Expect = 2e-17
 Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 17/102 (16%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD--------VLIMKDPITQR 201
           G          +  +FV GL    + E + +YF   G +          + +  D  T +
Sbjct: 2   GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HAT 238
            +G   ++F +P + +      I   DGK+          AT
Sbjct: 62  LKGEATVSFDDPPSAKAA----IDWFDGKEFSGNPIKVSFAT 99

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 8/75 (10%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--------MLMDQQTKRH 290
             +     +    IFV G+ ++ + E V  YF Q G ++           +  D++T + 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 291 RGFGFVTFENEEVVD 305
           +G   V+F++     
Sbjct: 63  KGEATVSFDDPPSAK 77

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 79.0 bits (194), Expect = 3e-17
 Identities = 23/201 (11%), Positives = 56/201 (27%), Gaps = 50/201 (24%)

Query: 161 SAKLFVGGLSWQTSSE-KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           S  L V GL     +  ++   F ++G V  V  MK        G   +  A+   V++ 
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRA 58

Query: 220 LKVPIHTLDGKKI---------------------------------------DPKHATPK 240
               I  L+   +                                               
Sbjct: 59  ----ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
            + +I + +  +       + + E       + G    T + +          G + +++
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDS 174

Query: 301 -EEVVDHICEIHFHMIKNKKV 320
             + ++ +  ++ + +KN   
Sbjct: 175 KSDALETLGFLNHYQMKNPNG 195

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 54.7 bits (131), Expect = 7e-09
 Identities = 8/77 (10%), Positives = 17/77 (22%), Gaps = 4/77 (5%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
             S  L       + + E   E     G      +            G + +       +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 219 VLKVPIHTLDGKKIDPK 235
            L      L+  ++   
Sbjct: 181 TLG----FLNHYQMKNP 193

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

 Score = 75.2 bits (185), Expect = 4e-17
 Identities = 13/95 (13%), Positives = 36/95 (37%), Gaps = 1/95 (1%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +D  +  +++ G     + + ++E+    G V ++ + +    +  +G  F+ F   E+ 
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESA 65

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
           +K ++ P        +           K   R + 
Sbjct: 66  KKFVETPGQKYKETDLLILFKDDYFAKKNEERKQN 100

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

 Score = 75.2 bits (185), Expect = 4e-17
 Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 3/89 (3%)

Query: 242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           +  + NR+  +++ G   D + +++K +    G+V   + +     K  +G  FV F++ 
Sbjct: 6   KNDVKNRS--VYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSI 62

Query: 302 EVVDHICEIHFHMIKNKKVECKKAQPKEA 330
           E      E      K   +         A
Sbjct: 63  ESAKKFVETPGQKYKETDLLILFKDDYFA 91

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

 Score = 74.5 bits (184), Expect = 5e-17
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           + ++FV  L +  + + L++ F   G V    I  +    +S+G G + F  PE  E+  
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 65

Query: 221 -KVPIHTLDGKKIDPKHATPKNRPKIG 246
             +    L G++ID +     + P  G
Sbjct: 66  RMMNGMKLSGREIDVRIDRNASGPSSG 92

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

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 16/85 (18%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
            +   +IFV  +  D + + +K  F++ G V    + M+    + +G G V FE+ EV +
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62

Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
                ++   +  ++++ +  +   
Sbjct: 63  RACRMMNGMKLSGREIDVRIDRNAS 87

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

 Score = 75.1 bits (185), Expect = 7e-17
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 17/97 (17%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFI 208
           D+  +  +FV GL    + E + +YF   G +          + +  D  T + +G   +
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 209 TFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPK 240
           +F +P + +      I   DGK+          AT +
Sbjct: 63  SFDDPPSAKAA----IDWFDGKEFSGNPIKVSFATRR 95

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

 Score = 65.1 bits (159), Expect = 3e-13
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 8/66 (12%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--------MLMDQQTKRHRGFGFVTFE 299
               IFV G+ ++ + E V  YF Q G ++           +  D++T + +G   V+F+
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 300 NEEVVD 305
           +     
Sbjct: 66  DPPSAK 71

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 75.7 bits (186), Expect = 1e-16
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
                   P   K++VG L    +  +L   FG +G +  V + ++P      GF F+ F
Sbjct: 63  HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEF 117

Query: 211 AEPETVEKVLKVPIHTLDGKKID 233
            +P          +  LDG+ + 
Sbjct: 118 EDPRDAADA----VRELDGRTLC 136

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 65.3 bits (159), Expect = 5e-13
 Identities = 21/118 (17%), Positives = 38/118 (32%), Gaps = 21/118 (17%)

Query: 200 QRSRGFGFITFAEPETVEKVLK---------------VPIHTLDGKKIDPKHATPKNRPK 244
           +  +G       +  T EKV K                   T    +    H    +R  
Sbjct: 10  KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDS 69

Query: 245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
                K ++VG +  + +  E++  F  +G +    +      +   GF FV FE+  
Sbjct: 70  CPLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPR 121

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
            +     L++  L      ++L      FG V    I++D  +  SRG GF      E  
Sbjct: 21  QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKC 79

Query: 217 EKVLKVPIHTLDGKKIDPK 235
           E V    I   +GK I   
Sbjct: 80  EAV----IGHFNGKFIKTP 94

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
            +++  +      +E++     FG+V  T +L D  +   RG GF   E+ E  +  I  
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGH 85

Query: 310 IHFHMIKNKKVECKKAQPKEAVQAN 334
            +   IK         +P     + 
Sbjct: 86  FNGKFIKTPPGVSAPTEPLLCKFSG 110

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 26/107 (24%), Positives = 43/107 (40%), Gaps = 25/107 (23%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG++        S KL VG +S   ++++LR  F  +G V +  I+        + 
Sbjct: 2   SSGSSGKA--------STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KD 45

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIG 246
           + F+     E   +     I  LD  +   K      +T + R   G
Sbjct: 46  YAFVHMERAEDAVEA----IRGLDNTEFQGKRMHVQLSTSRLRTASG 88

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 9/85 (10%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV 304
           G  + K+ VG +S   + +E++A F ++G V E   ++       + + FV  E  E+ V
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIE-CDIV-------KDYAFVHMERAEDAV 58

Query: 305 DHICEIHFHMIKNKKVECKKAQPKE 329
           + I  +     + K++  + +  + 
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLSTSRL 83

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 76.1 bits (187), Expect = 2e-16
 Identities = 32/204 (15%), Positives = 67/204 (32%), Gaps = 45/204 (22%)

Query: 161 SAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           ++ L V  L+  + + + L   FG++G V  V I+ +      +    +  A+    +  
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57

Query: 220 LK-VPIHTLDGKKIDPKHAT--------------------------------PKNRPKIG 246
           +  +  H L GK I    +                                  KN   I 
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVD 305
             +  + +  +    S E++K  FS  G V +      +     R    +   + EE V 
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQ 173

Query: 306 HICEIH-FHMIKNKKVECKKAQPK 328
            + ++H   + +N  +    ++  
Sbjct: 174 ALIDLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 50.3 bits (120), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 24/87 (27%), Gaps = 8/87 (9%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G        P SA L +  +    S E L+  F   G V           Q+ R    I 
Sbjct: 109 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQ 164

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKH 236
               E   + L      L    +   H
Sbjct: 165 MGSVEEAVQAL----IDLHNHDLGENH 187

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 40.3 bits (94), Expect = 4e-04
 Identities = 10/87 (11%), Positives = 31/87 (35%), Gaps = 9/87 (10%)

Query: 245 IGNRTKKIFVGGVSQDT-SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
           +GN    + V  ++ +  + + +   F  +G V+   +L        +    V   +   
Sbjct: 1   MGNSV--LLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQ 53

Query: 304 VDH-ICEIHFHMIKNKKVECKKAQPKE 329
               +  ++ H +  K +    ++ + 
Sbjct: 54  AQLAMSHLNGHKLHGKPIRITLSKHQN 80

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 73.7 bits (181), Expect = 3e-16
 Identities = 20/113 (17%), Positives = 42/113 (37%)

Query: 233 DPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
            P                 +++ G+  +   + V  +F +   VE+++ +      +  G
Sbjct: 9   SPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 68

Query: 293 FGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
            GFV F NE         H   + N+ ++      K  ++   ++ KR+  GP
Sbjct: 69  EGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGP 121

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 64.5 bits (157), Expect = 5e-13
 Identities = 21/110 (19%), Positives = 41/110 (37%), Gaps = 2/110 (1%)

Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD-VLIMKDPITQR 201
           GKS     RS           +++ GL ++  ++ + ++F     V D + I   P   +
Sbjct: 7   GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGK 65

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
           + G GF+ F      +  L      +  + I     T K   +  +  +K
Sbjct: 66  ATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRK 115

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

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 9/71 (12%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K++VG L       +L   F  +G +  V I ++P      GF F+ F +P   E     
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDA--- 53

Query: 223 PIHTLDGKKID 233
            +  LDGK I 
Sbjct: 54  -VRGLDGKVIC 63

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

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 5/52 (9%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           K++VG +       E++  FS +G +   V +     +   GF FV FE+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRT-VWIA----RNPPGFAFVEFEDPR 48

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 72.7 bits (179), Expect = 4e-16
 Identities = 19/98 (19%), Positives = 40/98 (40%), Gaps = 4/98 (4%)

Query: 147 GDSGRSTPTGDDPT--SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ-RSR 203
           G           P       F+G L +  + E ++E+F     ++ V + ++P    R +
Sbjct: 3   GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 61

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN 241
           GFG+  F + +++   L +   +L  ++I    A    
Sbjct: 62  GFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ 99

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 60.7 bits (148), Expect = 6e-12
 Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT-KRHRGFGFVTFENEEVVDHIC 308
              F+G +  D + E +K +F     +    +  +    +R +GFG+  FE+ + +    
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
            ++   + N+++    A   +
Sbjct: 79  SLNEESLGNRRIRVDVADQAQ 99

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 72.8 bits (179), Expect = 4e-16
 Identities = 24/116 (20%), Positives = 44/116 (37%), Gaps = 17/116 (14%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPI 198
           G SG S    +D  ++ ++V GL+   + + L ++F   G V          + I  D  
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 199 TQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
           T + +G   +++ +P T +      +   DGK           A  K     G  +
Sbjct: 61  TGKPKGDATVSYEDPPTAKAA----VEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 65.5 bits (160), Expect = 1e-13
 Identities = 16/102 (15%), Positives = 41/102 (40%), Gaps = 9/102 (8%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--------MLMDQQTK 288
           +     P   +    I+V G++   + +++  +F Q G V+           + +D++T 
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 289 RHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
           + +G   V++E+       +        +  K++   A+ K 
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104

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

 Score = 72.2 bits (178), Expect = 4e-16
 Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 26/104 (25%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG +          K+FVG +S   +S++LR  F   G V +  ++K         
Sbjct: 2   SSGSSGNTW---------KIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------D 44

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRP 243
           + F+   +    +      I  L+GK++  K      +T   + 
Sbjct: 45  YAFVHMEKEADAKAA----IAQLNGKEVKGKRINVELSTKGQKK 84

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

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 9/82 (10%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHI 307
           T KIFVG VS   +++E+++ F + G+V E   ++       + + FV  E   +    I
Sbjct: 9   TWKIFVGNVSAACTSQELRSLFERRGRVIE-CDVV-------KDYAFVHMEKEADAKAAI 60

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
            +++   +K K++  + +   +
Sbjct: 61  AQLNGKEVKGKRINVELSTKGQ 82

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 71.9 bits (177), Expect = 5e-16
 Identities = 22/106 (20%), Positives = 37/106 (34%), Gaps = 23/106 (21%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S          KL++G LS   +++ LR+ FG                    G+ 
Sbjct: 1   GSSGSSGMN-------KLYIGNLSPAVTADDLRQLFGDRKLPLAG------QVLLKSGYA 47

Query: 207 FITFAEPETVEKVLKVPIHTLD------GKKIDPKHATPKNRPKIG 246
           F+ + +     +     I TL       GK ++  ++  K     G
Sbjct: 48  FVDYPDQNWAIRA----IETLSGKVELHGKIMEVDYSVSKKLRSSG 89

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
            K+++G +S   +A++++  F            +  Q     G+ FV + ++      I 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 309 EIHFHM-IKNKKVECKKAQPKE 329
            +   + +  K +E   +  K+
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKK 84

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 72.5 bits (178), Expect = 5e-16
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 1/95 (1%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
             N P   N    + + G+    S EE+  +FS    V   + L      R  G  FV F
Sbjct: 6   SGNSPDTAN-DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 299 ENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
            ++E+ +   + H   I ++ +E  K+   E   +
Sbjct: 65  ASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTS 99

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 69.8 bits (171), Expect = 4e-15
 Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 3/96 (3%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG S  T +D     + + GL +  S E++ ++F     V + + +      RS G
Sbjct: 2   SSGSSGNSPDTANDGF---VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG 58

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPK 240
             F+ FA  E  EK LK     +  + I+   ++  
Sbjct: 59  EAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRA 94

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 71.4 bits (175), Expect = 1e-15
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDP-ITQRSRGFGFITFAEPETVE--- 217
           +LF+GG+      E++ E        V DV++        ++RGF F+ +          
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRPK 244
           + L      L G +I    A P+    
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAEPEIDVD 96

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.3 bits (154), Expect = 9e-13
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM--DQQTKRHRGFGFVTFENEEVVDHIC 308
           ++F+GG+ +    EE+    ++  +    V++        ++RGF FV +E+        
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 309 EI---HFHMIKNKKVECKKAQPKEAVQ 332
                    +   ++    A+P+  V 
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAEPEIDVD 96

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

 Score = 70.7 bits (174), Expect = 1e-15
 Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 21/102 (20%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G S  +G      KLF+G L  + + +++R  F  +G V +  I+K         +GF+ 
Sbjct: 1   GSSGSSG----MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVH 48

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIG 246
             +    E      I  L   K+         +  K++   G
Sbjct: 49  IEDKTAAEDA----IRNLHHYKLHGVNINVEASKNKSKASSG 86

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

 Score = 63.4 bits (155), Expect = 6e-13
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 9/83 (10%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
              K+F+G + ++ + +E+++ F Q+GKV E   ++       + +GFV  E+     D 
Sbjct: 7   GMVKLFIGNLPREATEQEIRSLFEQYGKVLE-CDII-------KNYGFVHIEDKTAAEDA 58

Query: 307 ICEIHFHMIKNKKVECKKAQPKE 329
           I  +H + +    +  + ++ K 
Sbjct: 59  IRNLHHYKLHGVNINVEASKNKS 81

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S  +   P    + V  + +  S +++ ++F  +  +   + +K        G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
            + F   +     +      L+ + I 
Sbjct: 61  MVAFESRDEATAAVI----DLNDRPIG 83

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
               I V  +    S +E+  +F  +  +  +V L   +     G   V FE+ +E    
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 307 ICEIHFHMIKNKKVECKKA 325
           + +++   I ++KV+    
Sbjct: 74  VIDLNDRPIGSRKVKLSGP 92

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

 Score = 72.7 bits (178), Expect = 6e-15
 Identities = 34/210 (16%), Positives = 67/210 (31%), Gaps = 44/210 (20%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
            S     + P      ++ L V  L+  + + + L   FG++G V  V I+ +      +
Sbjct: 18  GSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KK 72

Query: 204 GFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT------------------------ 238
               +  A+    +  +  +  H L GK I    +                         
Sbjct: 73  ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132

Query: 239 --------PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH 290
                    KN   I   +  + +  +    S E++K  FS  G V +         ++ 
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKD 188

Query: 291 RGFGFVTFEN-EEVVDHICEIHFHMIKNKK 319
           R    +   + EE V  + ++H H +    
Sbjct: 189 RKMALIQMGSVEEAVQALIDLHNHDLGENH 218

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 68.1 bits (167), Expect = 1e-14
 Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S  +   P    + V  + +  S +++ ++F  +  +   + +K        G  
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
            + F   +     +      L+ + I 
Sbjct: 61  MVAFESRDEATAAVI----DLNDRPIG 83

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
               I V  +    S +E+  +F  +  +  +V L   +     G   V FE+ +E    
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 307 ICEIHFHMIKNKKVECKKAQPKEA 330
           + +++   I ++KV+        +
Sbjct: 74  VIDLNDRPIGSRKVKLVLGSGPSS 97

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

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 17/91 (18%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
            + ++ +LFV          +L E FG FG + +V I+         GF F+ F E E+ 
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESA 78

Query: 217 EKVLKVPIHTLDGKKIDPK-----HATPKNR 242
            K     I  + GK    +     ++    +
Sbjct: 79  AKA----IEEVHGKSFANQPLEVVYSKLPAK 105

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

 Score = 63.9 bits (156), Expect = 6e-13
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 9/97 (9%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
           P+ +   +R +      ++FV     D    E+   F  FG ++E V ++        GF
Sbjct: 16  PRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE-VKIL-------NGF 67

Query: 294 GFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            FV FE  E     I E+H     N+ +E   ++   
Sbjct: 68  AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA 104

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 68.2 bits (167), Expect = 2e-14
 Identities = 11/102 (10%), Positives = 33/102 (32%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S     +       +  + +  +   + ++        + + +      +  G  
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNR 248
            + F   +   K  ++    L+G++      T ++  +I   
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKN 102

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 66.7 bits (163), Expect = 7e-14
 Identities = 9/87 (10%), Positives = 27/87 (31%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             + +      +  +    +  +V  +       E  V ++     +  G   V F+NE+
Sbjct: 9   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 68

Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKE 329
                  +H   +  ++        ++
Sbjct: 69  DARKSERLHRKKLNGREAFVHVVTLED 95

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 66.5 bits (163), Expect = 5e-14
 Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 19/89 (21%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG +           LFV  L+   + E L + F  FG +  V  +KD        
Sbjct: 2   SSGSSGMAKVK-------VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------- 46

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
           + FI F E +   K ++     ++GK ++
Sbjct: 47  YAFIHFDERDGAVKAME----EMNGKDLE 71

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 21/99 (21%), Positives = 47/99 (47%), Gaps = 9/99 (9%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
           + K +FV  ++   + E ++  FSQFGK+E          K+ + + F+ F+  +  V  
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKLER--------VKKLKDYAFIHFDERDGAVKA 61

Query: 307 ICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
           + E++   ++ + +E   A+P +  +      ++   GP
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 66.7 bits (163), Expect = 5e-14
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
            +         + L   F   G V ++    D  T +++GF F+        +K++K   
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS-- 73

Query: 225 HTLDGKKIDPKH 236
               GK++D KH
Sbjct: 74  --FHGKRLDLKH 83

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 11/50 (22%), Positives = 21/50 (42%)

Query: 253 FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
            +         + + + FS+ GKV      +D+ T + +GF FV   +  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 66.6 bits (163), Expect = 7e-14
 Identities = 16/115 (13%), Positives = 44/115 (38%), Gaps = 15/115 (13%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           +  L++  L ++ ++E++ + FG +G +  + +   P    +RG  ++ + +    +   
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNA- 63

Query: 221 KVPIHTLDGKKIDPKHATPKNRP-KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG 274
              +  L G  +        NR   +           +      E++K    ++G
Sbjct: 64  ---VDHLSGFNVS-------NRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYG 108

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 12/98 (12%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE---- 302
           NR   +++  +    +AEE+   F ++G + + + + +  T   RG  +V +E+      
Sbjct: 8   NRI--LYIRNLPYKITAEEMYDIFGKYGPIRQ-IRVGN--TPETRGTAYVVYEDIFDAKN 62

Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
            VDH+   +     N+ +         A Q      K 
Sbjct: 63  AVDHLSGFNVS---NRYLVVLYYNANRAFQKMDTKKKE 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 66.3 bits (162), Expect = 8e-14
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 12/96 (12%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSS------EKLREYFGMFGAVTDVLIMKDPITQ 200
           GD  +  P   D   + + V  +              + + F  FG +T+    ++    
Sbjct: 1   GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DG 58

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH 236
           +++G+ F+ +A P      +K      DG K+D +H
Sbjct: 59  KTKGYIFLEYASPAHAVDAVK----NADGYKLDKQH 90

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 8/59 (13%)

Query: 250 KKIFVGGVSQDTSA------EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             I V  V Q            +   FS+FGK+        ++  + +G+ F+ + +  
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPA 72

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 9/84 (10%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G S  +G+D T   L+VGGL    +   LR +F  FG +  + +++       +   FI 
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54

Query: 210 FAEPETVEKVLKVPIHTLDGKKID 233
           FA  +  E   +    + +   ++
Sbjct: 55  FATRQAAEVAAE---KSFNKLIVN 75

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 10/56 (17%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
             T  ++VGG+    +  +++ +F QFG++    ++        +   F+ F   +
Sbjct: 12  ITT--LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQ 59

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 65.2 bits (159), Expect = 2e-13
 Identities = 26/112 (23%), Positives = 44/112 (39%), Gaps = 4/112 (3%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG+  P   D     + V G+ +      +R++F     V  V ++KD    R+ G
Sbjct: 2   SSGSSGKPLPINPDDLY--VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNG 57

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGG 256
            G + F  P+   + LK     +  + ++   AT +     G         G
Sbjct: 58  NGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 59.8 bits (145), Expect = 2e-11
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           + V G+       +V+ +F    +V+   +L D    R+ G G V F + +      + +
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVG-RNNGNGLVKFLSPQDTFEALKRN 76

Query: 312 FHMIKNKKVECKKAQPKEAVQA 333
             ++  + VE   A  ++ V A
Sbjct: 77  RMLMIQRYVEVSPATERQWVAA 98

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 65.7 bits (160), Expect = 2e-13
 Identities = 17/91 (18%), Positives = 35/91 (38%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
             +          + + G+    + EE+  +FS    V   + L      +  G  FV F
Sbjct: 32  RGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQF 91

Query: 299 ENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            ++E+ +     H   I ++ +E  K+  +E
Sbjct: 92  ASQELAEKALGKHKERIGHRYIEVFKSSQEE 122

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 65.3 bits (159), Expect = 3e-13
 Identities = 26/122 (21%), Positives = 50/122 (40%), Gaps = 24/122 (19%)

Query: 148 DSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGF 207
             GR + + D      + + GL +  + E++ ++F     V + + +      +  G  F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 208 ITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK 267
           + FA  E  EK L                   K++ +IG+R  ++F       +S EEV+
Sbjct: 89  VQFASQELAEKALG------------------KHKERIGHRYIEVFK------SSQEEVR 124

Query: 268 AY 269
           +Y
Sbjct: 125 SY 126

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 64.7 bits (158), Expect = 2e-13
 Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 20/108 (18%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S  +    T   + + GL ++ +   +  +F        V I   P   R  G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEA 58

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFV 254
            + FA  E     +                   K++  + +R  ++F+
Sbjct: 59  DVEFATHEDAVAAMA------------------KDKANMQHRYVELFL 88

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 11/82 (13%), Positives = 25/82 (30%), Gaps = 2/82 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
           + + G+    +  ++  +FS    +   V +      R  G   V F   E         
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75

Query: 312 FHMIKNKKVECKKAQPKEAVQA 333
              ++++ VE           +
Sbjct: 76  KANMQHRYVELFLNSTAGTSGS 97

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 16/87 (18%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G++ PT       +L+VGGL   TS   L   F  FG++  +         +   F +I 
Sbjct: 12  GKANPT------TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQ 59

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKH 236
           +   +  +         + G  +    
Sbjct: 60  YESLDAAQAACA----KMRGFPLGGPD 82

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 10/67 (14%)

Query: 240 KNRPKIG----NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF 295
            +  KIG    N T +++VGG+  +TS   +   F +FG +     +      +   F +
Sbjct: 4   GSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAY 57

Query: 296 VTFENEE 302
           + +E+ +
Sbjct: 58  IQYESLD 64

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.7 bits (158), Expect = 3e-13
 Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 17/96 (17%)

Query: 145 SSGDSGRSTPTG-------DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP 197
           SSG SG +             P +  ++ GG++   + + +R+ F  FG + ++ +  + 
Sbjct: 2   SSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE- 60

Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
                +G+ F+ F+  E+        I +++G  I+
Sbjct: 61  -----KGYSFVRFSTHESAAHA----IVSVNGTTIE 87

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
           ++ GG++   + + ++  FS FG++ E  +  +      +G+ FV F   E   H I  +
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81

Query: 311 HFHMIKNKKVECKKAQPKEAVQAN 334
           +   I+   V+C   +    + + 
Sbjct: 82  NGTTIEGHVVKCYWGKESPDMTSG 105

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 18/99 (18%), Positives = 43/99 (43%), Gaps = 11/99 (11%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
           ++ + R      T  ++V G  +D +   ++  FS FG + +            R   FV
Sbjct: 5   SSGERRAPRKGNT--LYVYG--EDMTPTLLRGAFSPFGNIIDL------SMDPPRNCAFV 54

Query: 297 TFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQAN 334
           T+E  E  D  + E++   +++ +++   A+ +  + + 
Sbjct: 55  TYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 12/87 (13%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S           L+V G     +   LR  F  FG + D+ +         R   
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCA 52

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
           F+T+ + E+ ++     +  L+G +++
Sbjct: 53  FVTYEKMESADQA----VAELNGTQVE 75

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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 13/99 (13%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFI 208
           G S  +G +     LFVG L+       L E+F  ++ +     ++ D  T  S+G+GF+
Sbjct: 1   GSSGSSGPE---YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFV 56

Query: 209 TFAEPETVEKVL-----KVPIHTLDGKKIDPKHATPKNR 242
            F +    ++ L      V    L  K +    A PK  
Sbjct: 57  KFTDELEQKRALTECQGAVG---LGSKPVRLSVAIPKAS 92

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

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
           +FVG ++ D     +  +F +         ++  QT   +G+GFV F +E      + E 
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71

Query: 311 HFHM-IKNKKVECKKAQPKE 329
              + + +K V    A PK 
Sbjct: 72  QGAVGLGSKPVRLSVAIPKA 91

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 69.1 bits (168), Expect = 5e-13
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           LFV  +++ T+  KLR  F ++G +  + ++    + + RG+ FI +         +   
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER----DMHSA 160

Query: 224 IHTLDGKKID 233
               DGKKID
Sbjct: 161 YKHADGKKID 170

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 69.1 bits (168), Expect = 5e-13
 Identities = 20/92 (21%), Positives = 44/92 (47%), Gaps = 2/92 (2%)

Query: 239 PKNRPKI-GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
           P N P   G+  K +FV  V+ DT+  +++  F  +G ++   M+  +++ + RG+ F+ 
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150

Query: 298 FENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
           +E+E  +           I  ++V     + +
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182

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

 Score = 63.0 bits (154), Expect = 8e-13
 Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 18/102 (17%)

Query: 153 TPTGDDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
           T   + P  ++LF+G L  +  S++ L   F  +G +  + I           FGFI F 
Sbjct: 2   TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD 53

Query: 212 EPETVEKVLKVPIHTLDGK-----KIDPKHATPKNRPKIGNR 248
            P++V       I     +     K+  + ++   RP+  + 
Sbjct: 54  NPQSVRDA----IECESQEMNFGKKLILEVSSSNARPQFDHG 91

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 249 TKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
             ++F+G +  ++ S E++   FS +G + +  +           FGF+ F+N + V   
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDA 61

Query: 307 ICEIHFHMIKNKKVECKKAQPK 328
           I      M   KK+  + +   
Sbjct: 62  IECESQEMNFGKKLILEVSSSN 83

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 63.4 bits (154), Expect = 1e-12
 Identities = 20/100 (20%), Positives = 39/100 (39%), Gaps = 3/100 (3%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV---EETVMLMDQQTKRHRGF 293
           +    +         + + G+    +AEEV A+F Q   +   +E ++ +     R  G 
Sbjct: 11  SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70

Query: 294 GFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
            FV F  EE   +    H  ++  + +E  ++   E  Q 
Sbjct: 71  AFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQV 110

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 58.0 bits (140), Expect = 8e-11
 Identities = 22/113 (19%), Positives = 41/113 (36%), Gaps = 5/113 (4%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG----MFGAVTDVLIMKDP 197
                G S              + + GL +  ++E++  +FG    + G    +L +  P
Sbjct: 4   GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63

Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTK 250
              R  G  F+ FA  E  +  L+     L  + I+   +T     ++ NR  
Sbjct: 64  -DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFS 115

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

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 19/107 (17%), Positives = 36/107 (33%), Gaps = 18/107 (16%)

Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIMKDPITQ 200
           +                   ++LF+G L  +  S++ L   F  +G +  + I       
Sbjct: 3   SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN----- 57

Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGK-----KIDPKHATPKNR 242
               FGFI F  P++V       I     +     K+  + ++   R
Sbjct: 58  ---AFGFIQFDNPQSVRDA----IEXESQEMNFGKKLILEVSSSNAR 97

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 12/104 (11%)

Query: 229 GKKIDPKHATPKNRPKIGNRTKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQT 287
           G      H +    P+  +   ++F+G +  ++ S E++   FS +G + +  +      
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------ 55

Query: 288 KRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKK--VECKKAQPK 328
                FGF+ F+N + V   I      M   KK  +E   +  +
Sbjct: 56  --KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 11/87 (12%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S       +  ++ V GL    S + L+++    G V    + +D       G G
Sbjct: 1   GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 53

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
            + F   E +       +  LD  K  
Sbjct: 54  VVEFVRKEDMTYA----VRKLDNTKFR 76

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 52.1 bits (125), Expect = 7e-09
 Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 8/92 (8%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
               P       ++ V G+    S +++K +  + G V    +  D       G G V F
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEF 57

Query: 299 ENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
             +E + + + ++     ++ + E    + K 
Sbjct: 58  VRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV 89

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

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 13/76 (17%), Positives = 21/76 (27%), Gaps = 10/76 (13%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
            P     ++G +    +   L   F  FG + D     +      +G  FI +   E   
Sbjct: 24  PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAA 77

Query: 218 KVLKVPIHTLDGKKID 233
                 I  L      
Sbjct: 78  VC----IVALANFPFQ 89

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 11/100 (11%), Positives = 30/100 (30%), Gaps = 11/100 (11%)

Query: 234 PKHATPKNRPKIGNRTK----KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR 289
           P    P+    I           ++G +    +  ++   F  FG + +           
Sbjct: 8   PPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------P 61

Query: 290 HRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
            +G  F+ ++  E     I  +     + + +     + +
Sbjct: 62  EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 60.6 bits (147), Expect = 6e-12
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 9/91 (9%)

Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
           G S      S P    P +A ++VG L        L+      G+V   L       Q  
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRL-----TWQGP 55

Query: 203 RGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
           R   F+ + +    ++ +      L G ++ 
Sbjct: 56  RRRAFLHYPDSAAAQQAVS----CLQGLRLG 82

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 12/99 (12%), Positives = 32/99 (32%), Gaps = 7/99 (7%)

Query: 233 DPKHATPKNRPKIGNRTK-KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR 291
               + P + P  G      ++VG + +D    ++K    + G V      +    +  R
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPR 56

Query: 292 GFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
              F+ + +       +  +    +    +    A+ + 
Sbjct: 57  RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR 95

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 60.6 bits (147), Expect = 9e-12
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 15/88 (17%)

Query: 164 LFVGGLSWQTSSE---KLREYFGMFGAVTDVLIMKDPIT---QRSRGFGFITFAEPETVE 217
           +FV GLS + +     K  EYFG FG +  V+I         Q      ++T+   E   
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 218 KVLKVPIHTLDGKKIDPK-----HATPK 240
           +     I  ++   +D +       T K
Sbjct: 78  RA----IQCVNNVVVDGRTLKASLGTTK 101

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.4 bits (136), Expect = 3e-10
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 252 IFVGGVSQDTSAEEV---KAYFSQFGKVEETVMLMDQQT---KRHRGFGFVTFENEEVVD 305
           +FV G+SQ  +  EV     YF +FGK+ + V+         +      +VT+   E   
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 306 H-ICEIHFHMIKNKKVECKKAQPK 328
             I  ++  ++  + ++      K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 60.1 bits (146), Expect = 1e-11
 Identities = 20/114 (17%), Positives = 39/114 (34%), Gaps = 21/114 (18%)

Query: 145 SSGDSGRSTPTG---------DDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIM 194
           SSG SG S                 ++++F+G L+     +  +   F  +G V    + 
Sbjct: 2   SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH 61

Query: 195 KDPITQRSRGFGFITFAEPETVEKVLKVPIH--TLDGKKIDPKHATPKNRPKIG 246
           K        G+ F+ ++        +    +   L G+ +D   A      + G
Sbjct: 62  K--------GYAFVQYSNERHARAAVLG-ENGRVLAGQTLDINMAGEPKPDRSG 106

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 58.2 bits (141), Expect = 6e-11
 Identities = 21/100 (21%), Positives = 44/100 (44%), Gaps = 12/100 (12%)

Query: 231 KIDPKHATPKNRPKIGNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKR 289
           K+   + T KN PK  N   ++F+G ++       +V+  FS++G+V    +        
Sbjct: 11  KLQASNVTNKNDPKSINS--RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------- 60

Query: 290 HRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
           H+G+ FV + NE      +   +  ++  + ++   A   
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100

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

 Score = 59.8 bits (145), Expect = 1e-11
 Identities = 12/88 (13%), Positives = 33/88 (37%), Gaps = 4/88 (4%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
             R +K+ +  +      E + +   Q+G VE    +             VT+ +++   
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVVNVTYSSKDQAR 68

Query: 306 H-ICEIHFHMIKNKKVECKKAQPKEAVQ 332
             + +++   ++N  ++      + A Q
Sbjct: 69  QALDKLNGFQLENFTLKVAYIPDEMAAQ 96

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

 Score = 57.8 bits (140), Expect = 6e-11
 Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 7/87 (8%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S          KL +  +      E L      +G V     +            
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVV 57

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
            +T++  +   +     +  L+G +++
Sbjct: 58  NVTYSSKDQARQA----LDKLNGFQLE 80

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 13/69 (18%), Positives = 32/69 (46%), Gaps = 7/69 (10%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
           +   +  +++  L+ +   ++L++     F  FG + D+L+ +     + RG  F+ F E
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 60

Query: 213 PETVEKVLK 221
             +    L+
Sbjct: 61  VSSATNALR 69

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 22/104 (21%), Positives = 50/104 (48%), Gaps = 13/104 (12%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRG 292
           A P+ RP   N T  I++  +++    +E+K    A FS+FG++ + +++   ++ + RG
Sbjct: 1   AVPETRP---NHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD-ILVS--RSLKMRG 52

Query: 293 FGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
             FV F+      + +  +      +K +  + A+    + A +
Sbjct: 53  QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 59.5 bits (144), Expect = 4e-11
 Identities = 20/110 (18%), Positives = 35/110 (31%), Gaps = 20/110 (18%)

Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
           +    SG S  T    T   + + GL ++ +   +  +F        V I   P   R  
Sbjct: 29  QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVT 86

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIF 253
           G   + FA  E     +                   K+R  + +R  ++F
Sbjct: 87  GEADVEFATHEEAVAAMS------------------KDRANMQHRYIELF 118

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 12/100 (12%), Positives = 27/100 (27%), Gaps = 2/100 (2%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
            + +              + + G+    +  ++  +FS    V   V +      R  G 
Sbjct: 31  GRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRVTGE 88

Query: 294 GFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
             V F   E            ++++ +E        A   
Sbjct: 89  ADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNG 128

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 20/115 (17%), Positives = 41/115 (35%), Gaps = 27/115 (23%)

Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           G S  +G    +  + + G  +  + + + E+         + I+++       G+ F+ 
Sbjct: 1   GSSGSSGTTCHT--VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVD 56

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAE 264
           F+  E V++ LK                   NR  +G R   I    V ++ S  
Sbjct: 57  FSNEEEVKQALK------------------CNREYMGGR--YIE---VFREKSGP 88

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           G     + + G   + + + V  + +    V   + ++        G+ FV F NEE V 
Sbjct: 7   GTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA--IRIVRNAHGNKTGYIFVDFSNEEEVK 64

Query: 306 HICEIHFHMIKNKKVECKKAQPKEA 330
              + +   +  + +E  + +   +
Sbjct: 65  QALKCNREYMGGRYIEVFREKSGPS 89

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 57.9 bits (140), Expect = 6e-11
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 2/84 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKV--EETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           I   G+    + E+V  +FS       E  +  +  +  + RG   +  E+E+ V    E
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

Query: 310 IHFHMIKNKKVECKKAQPKEAVQA 333
            H   +  + VE  +   ++    
Sbjct: 74  KHRMYMGQRYVEVYEINNEDVDAL 97

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 11/91 (12%), Positives = 30/91 (32%), Gaps = 4/91 (4%)

Query: 164 LFVGGLSWQTSSEKLREYFGMF---GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           +   GL W  + E +  +F           +  + +    + RG   I     + V+K L
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMESEQDVQKAL 72

Query: 221 KVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
           +     +  + ++      ++   +    + 
Sbjct: 73  EKHRMYMGQRYVEVYEINNEDVDALMKSLQV 103

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 58.9 bits (142), Expect = 7e-11
 Identities = 16/99 (16%), Positives = 33/99 (33%), Gaps = 2/99 (2%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE--ETVMLMDQQTKRHRGFG 294
                    G     + + G+    S E+V+ + S     +    V  +  +  R  G  
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91

Query: 295 FVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
           FV   +E+ V    +     + ++ +E  K+   E    
Sbjct: 92  FVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWV 130

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 15/93 (16%), Positives = 28/93 (30%), Gaps = 4/93 (4%)

Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMF---GAVTDVLIMKDPIT 199
           G      G      +      + + GL W  S E ++ +            V  +     
Sbjct: 26  GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-E 84

Query: 200 QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI 232
            R  G  F+     + V+  LK    ++  + I
Sbjct: 85  GRQSGEAFVELGSEDDVKMALKKDRESMGHRYI 117

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.9 bits (135), Expect = 2e-10
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 12/79 (15%)

Query: 164 LFVGGL------SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           + V  +        +     + + F  FG +T+    ++    +++G+ F+ +A P    
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61

Query: 218 KVLKVPIHTLDGKKIDPKH 236
             +K      DG K+D +H
Sbjct: 62  DAVK----NADGYKLDKQH 76

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 8/57 (14%)

Query: 252 IFVGGVSQDTSA------EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           I V  V Q            +   FS+FGK+        ++  + +G+ F+ + +  
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPA 58

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 56.9 bits (137), Expect = 2e-10
 Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 2/96 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEET--VMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           + + G+    S E+V+ + S     +    V  +  +  R  G  FV  E+E+ V    +
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
                + ++ +E  K+   E        G     GP
Sbjct: 80  KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGP 115

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 55.3 bits (133), Expect = 6e-10
 Identities = 19/110 (17%), Positives = 37/110 (33%), Gaps = 5/110 (4%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG---MFGAVTDVLIMKDPITQR 201
           SSG SG      +      + + GL W  S E ++ +     +   V  V  +      R
Sbjct: 2   SSGSSGMM-LGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGR 59

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
             G  F+     + V+  LK    ++  + I+   +       +   +  
Sbjct: 60  QSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGP 109

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 15/92 (16%), Positives = 29/92 (31%), Gaps = 8/92 (8%)

Query: 143 GKSSGDSGRSTPTGDDP-TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
             SSG   R +     P    ++ +  L    S + L++        T         T+ 
Sbjct: 9   HHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRD 65

Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
             G G + F   E + +     +  L+  +  
Sbjct: 66  FDGTGALEFPSEEILVEA----LERLNNIEFR 93

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 53.3 bits (128), Expect = 3e-09
 Identities = 10/92 (10%), Positives = 33/92 (35%), Gaps = 4/92 (4%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
             +  K+  +  +I +  + +  S +++K    +              T+   G G + F
Sbjct: 18  GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDGTGALEF 74

Query: 299 ENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
            +EE++   +  ++    +   +  ++     
Sbjct: 75  PSEEILVEALERLNNIEFRGSVITVERDDNPP 106

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 56.0 bits (135), Expect = 4e-10
 Identities = 18/87 (20%), Positives = 30/87 (34%), Gaps = 12/87 (13%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
              GR  P     +  ++ V GL    S + L+++    G V    + +D       G G
Sbjct: 3   APRGRYGP-PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 54

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
            + F   E +       +  LD  K  
Sbjct: 55  VVEFVRKEDMTYA----VRKLDNTKFR 77

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 52.5 bits (126), Expect = 7e-09
 Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 8/91 (8%)

Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           +  P       ++ V G+    S +++K +  + G V    +  D       G G V F 
Sbjct: 7   RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV 59

Query: 300 NEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
            +E + + + ++     ++ + E    + K 
Sbjct: 60  RKEDMTYAVRKLDNTKFRSHEGETAYIRVKV 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 56.1 bits (135), Expect = 4e-10
 Identities = 12/89 (13%), Positives = 31/89 (34%), Gaps = 8/89 (8%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
               S  + +  ++ +   EKL+          G + D+++     +  + G  +I FA 
Sbjct: 25  HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFAT 81

Query: 213 PETVEKVLKVPIHT-LDGKKIDPKHATPK 240
            E+ +  ++        G  +    +   
Sbjct: 82  QESAQAFVEAFQGYPFQGNPLVITFSETP 110

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 49.5 bits (118), Expect = 1e-07
 Identities = 10/100 (10%), Positives = 35/100 (35%), Gaps = 8/100 (8%)

Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRH 290
                 + P     ++ + +  ++ +   E+++    A  S  G + + V+     +  +
Sbjct: 15  DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDN 71

Query: 291 RGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKAQPKE 329
            G  ++ F  +E      E    +  +   +    ++  +
Sbjct: 72  SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 57.5 bits (138), Expect = 5e-10
 Identities = 10/69 (14%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           +++ G     + + ++E+    G V ++ + +    +  +G  F+ F   E+ +K ++ P
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP 170

Query: 224 IHTLDGKKI 232
                   +
Sbjct: 171 GQKYKETDL 179

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 53.7 bits (128), Expect = 1e-08
 Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
                  +  K   + + +++ G   D + +++K +    G+V   + +     K  +G 
Sbjct: 94  KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVL-NIQMRRTLHKAFKGS 152

Query: 294 GFVTFENEE 302
            FV F++ E
Sbjct: 153 IFVVFDSIE 161

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 54.7 bits (132), Expect = 6e-10
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 8/83 (9%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           + +  I V  + QD++ +EV      +      V        R++   FVT  N E   +
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV-------DRNKRTAFVTLLNGEQAQN 55

Query: 307 -ICEIHFHMIKNKKVECKKAQPK 328
            I   H +  + K +  +     
Sbjct: 56  AIQMFHQYSFRGKDLIVQLQPTD 78

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 52.0 bits (125), Expect = 6e-09
 Identities = 9/73 (12%), Positives = 23/73 (31%), Gaps = 11/73 (15%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S+ + V  L   ++ +++ +    +        +K     R++   F+T    E  +   
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA- 56

Query: 221 KVPIHTLDGKKID 233
              I         
Sbjct: 57  ---IQMFHQYSFR 66

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 54.8 bits (132), Expect = 2e-09
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 15/83 (18%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFITFAE 212
           + +++V  L+     + L+  FG +   +        D+ +MK     R +G  FI    
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK---EGRMKGQAFIGLPN 101

Query: 213 PETVEKVLKVPIHTLDGKKIDPK 235
            +   K LK      +G  +  K
Sbjct: 102 EKAAAKALK----EANGYVLFGK 120

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 53.3 bits (128), Expect = 7e-09
 Identities = 15/131 (11%), Positives = 48/131 (36%), Gaps = 14/131 (10%)

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKI--------GNRTKKIFVGGVSQDTSAEEVKA 268
               ++P   +  ++++    + +    +        G    +I+V  +++    +++K 
Sbjct: 5   SDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKY 64

Query: 269 YFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVEC 322
            F ++             +   +  R +G  F+   NE+     + E + +++  K +  
Sbjct: 65  IFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV 124

Query: 323 KKAQPKEAVQA 333
           + A+     Q 
Sbjct: 125 QFARSARPKQD 135

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 53.4 bits (128), Expect = 3e-09
 Identities = 19/109 (17%), Positives = 43/109 (39%), Gaps = 11/109 (10%)

Query: 225 HTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD 284
           H      + P+ +   +    G  ++ I +  +  D +  EV +    FGKV   +ML  
Sbjct: 7   HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-- 64

Query: 285 QQTKRHRGFGFVTFENEE----VVDHICEIHFHMIKNKKVECKKAQPKE 329
               + +   F+    EE    +V++       +++ + +  + +  KE
Sbjct: 65  ----KGKNQAFIEMNTEEAANTMVNY-YTSVTPVLRGQPIYIQFSNHKE 108

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 17/109 (15%), Positives = 34/109 (31%), Gaps = 9/109 (8%)

Query: 135 AHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM 194
            H     +G     S           S  + +  L    +  ++      FG VT++L++
Sbjct: 5   HHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML 64

Query: 195 KDPITQRSRGFGFITFAEPETVEKVLKVPIHT---LDGKKIDPKHATPK 240
                 + +   FI     E    ++         L G+ I  + +  K
Sbjct: 65  ------KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.5 bits (126), Expect = 6e-09
 Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 18/89 (20%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SGRS           +    L   T + +++E F  FG++  VL+           
Sbjct: 2   SSGSSGRSKTV--------ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGI 47

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
              + F EP    K        L   K  
Sbjct: 48  TAIVEFLEPLEARK----AFRHLAYSKFH 72

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 8/57 (14%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
                 I    +   T A E++  FS+FG +   ++              V F    
Sbjct: 9   SKTV--ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPL 57

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 55.3 bits (132), Expect = 9e-09
 Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 11/86 (12%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
              +   +  +++  L+ +   ++L++     F  FG + D+L+ +     + RG  F+ 
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVI 58

Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPK 235
           F E  +        + ++ G     K
Sbjct: 59  FKEVSSATNA----LRSMQGFPFYDK 80

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 50.6 bits (120), Expect = 3e-07
 Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 13/104 (12%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRG 292
           A P+ RP   N T  I++  +++    +E+K    A FSQFG++ + ++    ++ + RG
Sbjct: 2   AVPETRP---NHT--IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRG 53

Query: 293 FGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
             FV F+      + +  +      +K +  + A+    + A +
Sbjct: 54  QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 50.6 bits (120), Expect = 3e-07
 Identities = 27/195 (13%), Positives = 49/195 (25%), Gaps = 9/195 (4%)

Query: 43  PPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVN 102
                + K+ G         +      Q TP  ++  Q                 +  + 
Sbjct: 89  TDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMT 148

Query: 103 GKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSA 162
                           P    +   GL   +     +       G    + P  ++P + 
Sbjct: 149 QAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNH 208

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            LF+  L  +T+   L   F  F    +V ++            F+ F            
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAA--- 260

Query: 223 PIHTLDGKKIDPKHA 237
               L G KI   +A
Sbjct: 261 -RDALQGFKITQNNA 274

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 11/76 (14%), Positives = 29/76 (38%), Gaps = 10/76 (13%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM-KDPI----TQRSRGFGFITFAEPETVE 217
           +L+VG + +  + E + ++F     +  +     +P+      + + F F+ F   +   
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 218 KVLKVPIHTLDGKKID 233
           + +       DG    
Sbjct: 68  QAMA-----FDGIIFQ 78

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 8/58 (13%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFENEE 302
           ++++VG +    + E +  +F+   ++          ++  Q  + + F F+ F + +
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64

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

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI- 307
           ++ I +  +  D +  EV +    FGKV   +ML      + +   F+    EE  + + 
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMV 69

Query: 308 --CEIHFHMIKNKKVECKKAQPKE 329
                   +++ + +  + +  KE
Sbjct: 70  NYYTSVTPVLRGQPIYIQFSNHKE 93

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

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 9/95 (9%)

Query: 149 SGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
           S      G    S  + +  L    +  ++      FG VT++L++K       +   FI
Sbjct: 4   SHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFI 57

Query: 209 TFAEPETVEKVLKVPIH---TLDGKKIDPKHATPK 240
                E    ++         L G+ I  + +  K
Sbjct: 58  EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 92

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 49.8 bits (119), Expect = 5e-08
 Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S        S  + V GL        L E    FG +  V++M        +   
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQA 54

Query: 207 FITFAEPETVEKVLK 221
            + F   ++ ++ + 
Sbjct: 55  LVEFENIDSAKECVT 69

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 11/89 (12%), Positives = 26/89 (29%), Gaps = 9/89 (10%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD--- 305
           +  + V G+ +     ++     +FG +   +M         +    V FEN +      
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECV 68

Query: 306 HICEIHFHMIKNKKVECKKAQPKEAVQAN 334
                    I  ++     +  K   +  
Sbjct: 69  TFAADVPVYIAGQQAFFNYSTSKRITRPG 97

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

 Score = 49.4 bits (118), Expect = 6e-08
 Identities = 13/78 (16%), Positives = 25/78 (32%), Gaps = 11/78 (14%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           P S  + + GL        L E    FG ++ V++M        +    + F +      
Sbjct: 19  PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACN 72

Query: 219 VLK----VPIHTLDGKKI 232
            +       I+ + G   
Sbjct: 73  AVNYAADNQIY-IAGHPA 89

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

 Score = 49.0 bits (117), Expect = 7e-08
 Identities = 9/70 (12%), Positives = 21/70 (30%), Gaps = 7/70 (10%)

Query: 234 PKHATPKNR-PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
             H       P     +  + + G+       ++     +FG +   V++        + 
Sbjct: 5   HHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKR 58

Query: 293 FGFVTFENEE 302
              V FE+  
Sbjct: 59  QALVEFEDVL 68

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 11/94 (11%)

Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
                 G  ++ + +  +  + +  EV A    FGKV   +ML      + +   F+   
Sbjct: 6   SGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELA 59

Query: 300 NEE----VVDHICEIHFHMIKNKKVECKKAQPKE 329
            EE    +V++   +  H ++N+ +  + +  KE
Sbjct: 60  TEEAAITMVNYYSAVTPH-LRNQPIYIQYSNHKE 92

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 9/97 (9%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S    D   S  L +  L  + +  ++      FG VT++L++K       +   
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQA 54

Query: 207 FITFAEPETVEKVLKVPIH---TLDGKKIDPKHATPK 240
           F+  A  E    ++         L  + I  +++  K
Sbjct: 55  FLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK 91

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 47.2 bits (112), Expect = 4e-07
 Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 6/51 (11%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           +  GG+    S  ++     + G V+  +M        ++ + F  +   E
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTE 74

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 11/81 (13%)

Query: 155 TGDDPTSA-KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
           T    T +  +  GGL    S  +L       G V  +L+  +      + + F  +   
Sbjct: 20  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTT 73

Query: 214 ETVEKVLKVPIHTLDGKKIDP 234
           E  ++       TL+GK++  
Sbjct: 74  EESKRA----YVTLNGKEVVD 90

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 43.3 bits (101), Expect = 1e-04
 Identities = 14/115 (12%), Positives = 26/115 (22%), Gaps = 3/115 (2%)

Query: 7   GGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAI 66
             A     Q         G + +P    +  +           +L+      T+   +  
Sbjct: 25  QPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMH 84

Query: 67  LHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTS 121
           LH  P   P    Q     Q              +   + G    +      P +
Sbjct: 85  LHNVPLVDPNAYMQPQVPVQMGTPLQQQQQP---MAAPAYGQPSAAMGQNMRPMN 136

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	398
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.98
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.91
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.87
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.83
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.82
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.8
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.79
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.79
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.79
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.79
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.79
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.77
2div_A	99	TRNA selenocysteine associated protein; structural	99.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.77
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.77
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.77
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.77
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.77
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.77
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.77
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.77
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.77
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.77
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.76
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.76
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.76
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.76
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.76
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.76
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.76
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.76
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.76
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.75
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.75
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.75
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.75
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.75
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.75
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.75
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.75
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.75
2div_A	99	TRNA selenocysteine associated protein; structural	99.75
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.75
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.75
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.74
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.74
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.74
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.74
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.74
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.74
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.74
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.74
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.74
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.73
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.73
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.73
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.73
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.73
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.73
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.73
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.73
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.72
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.72
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.72
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.72
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.72
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.71
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.71
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.71
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.71
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.55
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.71
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.71
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.71
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.71
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.71
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.71
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.71
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.71
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.71
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.71
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.71
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.71
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.7
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.7
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.7
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.7
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.7
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.7
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.7
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.7
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.7
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.7
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.69
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.69
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.69
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.69
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.69
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.69
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.69
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.68
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.68
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.68
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.68
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.68
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.67
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.67
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.67
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.67
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.67
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.66
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.66
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.66
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.65
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.65
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.65
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.65
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.45
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.64
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.64
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.64
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.63
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.63
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.63
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.62
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.62
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.62
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.62
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.61
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.61
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.61
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.6
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.6
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.58
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.58
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.58
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.57
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.57
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.57
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.56
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.56
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.55
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.55
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.54
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.53
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.52
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.52
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.5
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.48
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.45
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.41
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.37
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.35
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.34
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.33
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.29
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.2
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.19
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.15
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.13
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.02
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.93
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.92
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.89
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.88
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.72
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.65
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.5
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.2
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.2
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.7
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.65
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.46
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.44
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.37
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.34
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.3
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.07
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.01
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.98
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.82
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.52
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.27
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.25
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.1
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.94
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.11
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.87

>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=100.00  E-value=1.4e-37  Score=271.51  Aligned_cols=177  Identities=38%  Similarity=0.742  Sum_probs=154.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      +....++|||+|||.++|+++|+++|+.||.|.+|++++++.+|.++|||||+|.+.++|.+|++.++..++|+.|.+.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            44578999999999999999999999999999999999999999999999999999999999999989999999999998


Q ss_pred             CCCCCCCc---cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCc
Q psy6490         237 ATPKNRPK---IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFH  313 (398)
Q Consensus       237 ~~~~~~~~---~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~  313 (398)
                      +.......   .....++|||+|||.++|+++|+++|+.||.|++|+|+++..++.++|||||+|.+.++|.+|++.++.
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~  168 (196)
T 1l3k_A           89 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH  168 (196)
T ss_dssp             CCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCC
T ss_pred             ccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCc
Confidence            87654322   233457899999999999999999999999999999999988999999999999999999888888999


Q ss_pred             eeCCEEEEEEecCchHHHhh
Q psy6490         314 MIKNKKVECKKAQPKEAVQA  333 (398)
Q Consensus       314 ~i~g~~i~v~~a~~k~~~~~  333 (398)
                      .|+|+.|+|.|+.++++...
T Consensus       169 ~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          169 TVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             EETTEECEEEECC-------
T ss_pred             EECCEEEEEEecCChhHhcc
Confidence            99999999999999887654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=2.3e-37  Score=273.93  Aligned_cols=174  Identities=22%  Similarity=0.437  Sum_probs=154.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++|+++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|.+|++ +++..+.|+.|.+.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            367899999999999999999999999999999999999999999999999999999999998 8999999999998887


Q ss_pred             CCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         238 TPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       238 ~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      ...... .....++|||+||++++|+++|+++|++||.|++|+|++|.  +.++|||||+|.+.++|++|+ +|||..|+
T Consensus        93 ~~~~~~-~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~  169 (213)
T 4f02_A           93 QRDPSL-RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLN  169 (213)
T ss_dssp             CCCTHH-HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             cccccc-cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            654432 22345689999999999999999999999999999999984  457999999999988776665 69999999


Q ss_pred             CEEEEEEecCchHHHhhhh
Q psy6490         317 NKKVECKKAQPKEAVQANL  335 (398)
Q Consensus       317 g~~i~v~~a~~k~~~~~~~  335 (398)
                      |+.|+|.|+.++.++....
T Consensus       170 g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          170 DRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             TEECEEEECCCHHHHHHHH
T ss_pred             CEEEEEEEcCCCcccchhh
Confidence            9999999999988776543

>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=100.00  E-value=4.4e-37  Score=261.41  Aligned_cols=165  Identities=48%  Similarity=0.964  Sum_probs=153.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ++++|||+|||.++|+++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|++|++. ...++|+.|.+.++..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEcccccccc
Confidence            578999999999999999999999999999999999999999999999999999999999994 5689999999988765


Q ss_pred             CCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEE
Q psy6490         240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKK  319 (398)
Q Consensus       240 ~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~  319 (398)
                      +.   .....++|||+|||.++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|+++++..|+|+.
T Consensus        81 ~~---~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~  157 (167)
T 2cjk_A           81 RD---EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRK  157 (167)
T ss_dssp             HH---HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSC
T ss_pred             hh---hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeE
Confidence            43   234567899999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EEEEecCch
Q psy6490         320 VECKKAQPK  328 (398)
Q Consensus       320 i~v~~a~~k  328 (398)
                      |+|.|+.+|
T Consensus       158 i~V~~a~pk  166 (167)
T 2cjk_A          158 IEIKRAEPR  166 (167)
T ss_dssp             EEEEECCCC
T ss_pred             EEEeecCCC
Confidence            999999876

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.8e-35  Score=249.77  Aligned_cols=163  Identities=19%  Similarity=0.395  Sum_probs=149.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      ++|||+|||.++|+++|+++|+.||.|.++++++++ +++++|||||+|.+.++|.+|++ +++..+.|+.|.+.++...
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            689999999999999999999999999999999987 57799999999999999999995 8999999999999988765


Q ss_pred             CCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEE
Q psy6490         241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKK  319 (398)
Q Consensus       241 ~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~  319 (398)
                      .. ......++|||+|||.++|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|.+|+ +|||..|+|+.
T Consensus        80 ~~-~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  158 (166)
T 3md3_A           80 QQ-SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP  158 (166)
T ss_dssp             CC-CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CC-CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Confidence            54 33456788999999999999999999999999999999999999999999999999988777766 59999999999


Q ss_pred             EEEEecC
Q psy6490         320 VECKKAQ  326 (398)
Q Consensus       320 i~v~~a~  326 (398)
                      |+|.|++
T Consensus       159 i~v~~a~  165 (166)
T 3md3_A          159 LRINWAA  165 (166)
T ss_dssp             CEEEESC
T ss_pred             EEEEecC
Confidence            9999986

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

Probab=100.00  E-value=2.2e-35  Score=261.56  Aligned_cols=170  Identities=22%  Similarity=0.503  Sum_probs=152.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++ +++..++|+.|.|.+..
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            56899999999999999999999999999999999999899999999999999999999999 89999999999998876


Q ss_pred             CCCCCc--------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-H
Q psy6490         239 PKNRPK--------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-E  309 (398)
Q Consensus       239 ~~~~~~--------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~  309 (398)
                      ......        .....++|||+|||.++|+++|+++|++||.|++|+|+++..+++++|||||+|.+.++|.+|+ .
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence            554321        2245679999999999999999999999999999999999999999999999999987776666 5


Q ss_pred             HCCceeCCEEEEEEecCchH
Q psy6490         310 IHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       310 l~~~~i~g~~i~v~~a~~k~  329 (398)
                      |||..|+|+.|+|.|+.++.
T Consensus       187 l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          187 MNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HTTCBCSSSBCEEEECSSCS
T ss_pred             ccCCEeCCcEEEEEEecCCC
Confidence            99999999999999998764

>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=100.00  E-value=3.8e-35  Score=249.60  Aligned_cols=163  Identities=20%  Similarity=0.385  Sum_probs=151.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ++++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|++|++ +++..++|+.|.|.++.
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            56899999999999999999999999999999999999899999999999999999999998 89999999999999987


Q ss_pred             CCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC
Q psy6490         239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN  317 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g  317 (398)
                      ....   ....++|||+|||.++++++|+++|++||.|.++++.++..++.++|||||+|.+.++|.+++ .|||..|+|
T Consensus        82 ~~~~---~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A           82 PGGE---SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG  158 (168)
T ss_dssp             CCSS---TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             CCcc---cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecC
Confidence            6543   345678999999999999999999999999999999999889999999999999987776666 599999988


Q ss_pred             --EEEEEEec
Q psy6490         318 --KKVECKKA  325 (398)
Q Consensus       318 --~~i~v~~a  325 (398)
                        +.|+|+||
T Consensus       159 ~~~~l~V~~A  168 (168)
T 1b7f_A          159 GSQPLSVRLA  168 (168)
T ss_dssp             CSSCCEEEEC
T ss_pred             CCeEEEEEeC
Confidence              99999986

>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=100.00  E-value=6.2e-35  Score=247.84  Aligned_cols=162  Identities=26%  Similarity=0.488  Sum_probs=149.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      +++|||+|||.++++++|+++|+.||.|.++++++++.+|+++|||||+|.+.++|.+|++ +++..++|+.|.|.++.+
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            5899999999999999999999999999999999999999999999999999999999998 899999999999998876


Q ss_pred             CCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCE
Q psy6490         240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNK  318 (398)
Q Consensus       240 ~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~  318 (398)
                      ...   ....++|||+|||.++++++|+++|++||.|.++++.++..+|.++|||||+|.+.++|.+|+ +|||..|+|+
T Consensus        82 ~~~---~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           82 SSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CCG---GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             Ccc---cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            543   345678999999999999999999999999999999999889999999999999988776665 5999999997


Q ss_pred             E--EEEEec
Q psy6490         319 K--VECKKA  325 (398)
Q Consensus       319 ~--i~v~~a  325 (398)
                      .  |+|+||
T Consensus       159 ~~~i~v~~A  167 (167)
T 1fxl_A          159 TEPITVKFA  167 (167)
T ss_dssp             SSCCEEEEC
T ss_pred             ccceEEEeC
Confidence            5  888886

>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=100.00  E-value=2.4e-34  Score=265.96  Aligned_cols=211  Identities=13%  Similarity=0.178  Sum_probs=185.8

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      ..++++..+.+...+..++..+++....+....+...              ...++|||+|||.++|+++|+++|+.||.
T Consensus        56 ~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~--------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~  121 (284)
T 3smz_A           56 YKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ--------------PTDALLCVANLPPSLTQQQFEELVRPFGS  121 (284)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC--------------CCSCEEEEESCCTTCCHHHHHHHHGGGSC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEec--------------CCCCEEEEcCCCCcCCHHHHHHHHHhcCC
Confidence            3467889999999999888777766555555555431              14589999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCccCccccceeecCCCCCC-CHHH
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDT-SAEE  265 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~-tee~  265 (398)
                      |.++++++++.+|.++|||||+|.+.++|.+|++ +++..++|+.|.|.++..+.........++|||+|||.++ |+++
T Consensus       122 i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~  201 (284)
T 3smz_A          122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA  201 (284)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHH
T ss_pred             eeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcccCCccEEEEecCCcccCCHHH
Confidence            9999999999999999999999999999999995 8999999999999999887766666778899999999995 9999


Q ss_pred             HHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchHHHhh
Q psy6490         266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKEAVQA  333 (398)
Q Consensus       266 L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~~~~~  333 (398)
                      |+++|+.||.|.+|+|.++. +|.++|||||+|.+.++|.+|+ .|||..|+|+.|+|.|+.++..++.
T Consensus       202 l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~  269 (284)
T 3smz_A          202 LCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRS  269 (284)
T ss_dssp             HHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCHHH
T ss_pred             HHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcccc
Confidence            99999999999999999985 7999999999999987776665 6999999999999999998876543

>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=100.00  E-value=2.5e-33  Score=239.84  Aligned_cols=164  Identities=25%  Similarity=0.421  Sum_probs=141.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCC--CcccEEEEEEcChHhHHHHHh-CCCcccC---CcccC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ--RSRGFGFITFAEPETVEKVLK-VPIHTLD---GKKID  233 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~--~~~g~afV~f~~~e~a~~al~-~~~~~~~---g~~l~  233 (398)
                      +.++|||+|||.++|+++|+++|++||.|.+|++++++.++  +++|||||+|.+.++|++|++ +++..+.   ++.+.
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            57899999999999999999999999999999999998877  899999999999999999997 7776654   34444


Q ss_pred             CCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCC
Q psy6490         234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHF  312 (398)
Q Consensus       234 v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~  312 (398)
                      +.+.....  ......++|||+|||.++|+++|+++|++||.|+++++.++. +|.++|||||+|.+.++|.+|+ .|||
T Consensus        82 ~~~~~~~~--~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           82 MKPADSEK--NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGC--CSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Eccccccc--cccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            44443322  234467889999999999999999999999999999999995 6899999999999987776665 7999


Q ss_pred             ceeC---CEEEEEEecC
Q psy6490         313 HMIK---NKKVECKKAQ  326 (398)
Q Consensus       313 ~~i~---g~~i~v~~a~  326 (398)
                      ..+.   |+.|+|+||.
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            8776   4999999984

>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=100.00  E-value=4.6e-33  Score=237.71  Aligned_cols=158  Identities=19%  Similarity=0.421  Sum_probs=142.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcC----C-------CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMF----G-------AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD  228 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~----G-------~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~  228 (398)
                      +.++|||+|||.++|+++|+++|++|    |       .|.++++.+      ++|||||+|.+.++|++|+.+++..++
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHHHhCCcEec
Confidence            57999999999999999999999999    6       778887754      489999999999999999999999999


Q ss_pred             CcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q psy6490         229 GKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC  308 (398)
Q Consensus       229 g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~  308 (398)
                      |+.|.+.++.....   ....++|||+|||.++|+++|+++|++||.|.++++.+++.+|.++|||||+|.+.++|.+++
T Consensus        77 g~~i~v~~~~~~~~---~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~  153 (172)
T 2g4b_A           77 GQSLKIRRPHDYQP---LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI  153 (172)
T ss_dssp             TEECEEECCSSCCC---CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHH
T ss_pred             CceeeecCCcccCC---CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence            99999998765433   334788999999999999999999999999999999999889999999999999977776655


Q ss_pred             -HHCCceeCCEEEEEEecC
Q psy6490         309 -EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       309 -~l~~~~i~g~~i~v~~a~  326 (398)
                       .|||..|+|+.|+|+||.
T Consensus       154 ~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          154 AGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHTTCEETTEECEEEECC
T ss_pred             HHcCCCEECCeEEEEEeCC
Confidence             599999999999999973

>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=100.00  E-value=1e-33  Score=242.58  Aligned_cols=165  Identities=21%  Similarity=0.318  Sum_probs=144.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      .....++|||+|||.++|+++|+++|+.||.+.. .++.+..+++++|||||+|.+.++|.+|+++++..+.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEec
Confidence            3447899999999999999999999999997766 344455578899999999999999999999999999999999999


Q ss_pred             CCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee
Q psy6490         237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI  315 (398)
Q Consensus       237 ~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i  315 (398)
                      +..+.. ......++|||+|||.++|+++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|+ .|||..|
T Consensus        88 ~~~~~~-~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 1fje_B           88 PKGRDS-KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI  161 (175)
T ss_dssp             CCCSSC-STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEE
T ss_pred             CCCccc-cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            876544 234467899999999999999999999999988765     467899999999999988777666 5999999


Q ss_pred             CCEEEEEEecCch
Q psy6490         316 KNKKVECKKAQPK  328 (398)
Q Consensus       316 ~g~~i~v~~a~~k  328 (398)
                      +|+.|+|+|+.+|
T Consensus       162 ~g~~i~v~~a~~k  174 (175)
T 1fje_B          162 DGRSVSLYYTGEK  174 (175)
T ss_dssp             TTEEEEEEECSSC
T ss_pred             CCeEEEEEecCCC
Confidence            9999999999876

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=2.2e-32  Score=238.88  Aligned_cols=164  Identities=18%  Similarity=0.409  Sum_probs=143.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcC----C-------CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMF----G-------AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD  228 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~----G-------~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~  228 (398)
                      .+++|||+|||.++|+++|+++|+.|    |       .|.++++.      +++|||||+|.+.++|++|+++++..++
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHGGGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHHHhcCCEEc
Confidence            57999999999999999999999999    5       66666664      3589999999999999999999999999


Q ss_pred             CcccCCCCCCCCCCCc-----------------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcc
Q psy6490         229 GKKIDPKHATPKNRPK-----------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR  291 (398)
Q Consensus       229 g~~l~v~~~~~~~~~~-----------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~k  291 (398)
                      |+.|.|.++.......                 .....++|||+|||.++++++|+++|++||.|.+|++.++..++.++
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            9999999876542211                 12456899999999999999999999999999999999998899999


Q ss_pred             eEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchH
Q psy6490         292 GFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       292 g~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      |||||+|.+.++|.+++ .|||..|+|+.|+|.|+.++.
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999977666655 699999999999999998764

>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=100.00  E-value=3.2e-33  Score=259.37  Aligned_cols=204  Identities=14%  Similarity=0.218  Sum_probs=169.6

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCC-
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFG-  186 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G-  186 (398)
                      ..+++++.+.+...+..++. +++....+....+...               ..++|||+|||.++++++|+++|+.|| 
T Consensus        80 ~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~---------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~  143 (292)
T 2ghp_A           80 NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL---------------TECTLWMTNFPPSYTQRNIRDLLQDINV  143 (292)
T ss_dssp             SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC---------------CSCEEEEECCCTTCCHHHHHHHHHHTTC
T ss_pred             CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC---------------CCCEEEEECCCCCCCHHHHHHHHHHhCC
Confidence            45788999999999999994 7766555554444321               578999999999999999999999999 


Q ss_pred             CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCc----cCccccceeecCCCCC-
Q psy6490         187 AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK----IGNRTKKIFVGGVSQD-  260 (398)
Q Consensus       187 ~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~----~~~~~~~l~V~nLp~~-  260 (398)
                      .|.+|++++++. |.++|||||+|.+.++|.+|++ +++..++|+.|.|.++.+.....    .....++|||+|||.+ 
T Consensus       144 ~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~  222 (292)
T 2ghp_A          144 VALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTEL  222 (292)
T ss_dssp             CCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTT
T ss_pred             CeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCccc
Confidence            999999998875 7899999999999999999999 99999999999999887655432    3346689999999999 


Q ss_pred             CCHHHHHHHHhhcCCeeEEEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCch
Q psy6490         261 TSAEEVKAYFSQFGKVEETVMLMDQQ-TKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       261 ~tee~L~~~F~~~G~i~~v~i~~~~~-~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k  328 (398)
                      +|+++|+++|+.||.|.+|+|+++.. ++.++|||||+|.+.++|.+|+.|||..|+|+.|+|.|+.+|
T Consensus       223 ~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECCCC
T ss_pred             CCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEEEEecCC
Confidence            99999999999999999999999865 599999999999998777665599999999999999999876

>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=99.98  E-value=4.8e-32  Score=237.47  Aligned_cols=159  Identities=14%  Similarity=0.236  Sum_probs=135.5

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp-~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ++++|||+||+ .++|+++|+++|+.||.|.+|+++++     ++|||||+|.+.++|++|++ +++..+.|+.|.|.++
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            57899999999 89999999999999999999999876     38999999999999999998 9999999999999877


Q ss_pred             CCCCCCc----------------------------------cCccccceeecCCCCCCCHHHHHHHHhhcCCe--eEEEE
Q psy6490         238 TPKNRPK----------------------------------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV--EETVM  281 (398)
Q Consensus       238 ~~~~~~~----------------------------------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i--~~v~i  281 (398)
                      .......                                  ...+.++|||+|||+++|+++|+++|++||.|  .++++
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            5322100                                  01234579999999999999999999999999  89998


Q ss_pred             eecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCE----EEEEEec
Q psy6490         282 LMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNK----KVECKKA  325 (398)
Q Consensus       282 ~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~----~i~v~~a  325 (398)
                      +.+.  +.++|||||+|++.++| +|+..|||..|+|+    .+.|+||
T Consensus       158 ~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            8774  55679999999996665 55557999999987    5777765

>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=99.98  E-value=1.6e-31  Score=246.76  Aligned_cols=161  Identities=18%  Similarity=0.336  Sum_probs=140.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH----HHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLR----EYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~----~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      ...+++|||+|||.++|+++|+    ++|+.||.|.+|++.+   +++++|||||+|.+.++|++|++ +++..+.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4478999999999999999977    8999999999999886   67799999999999999999996 89999999999


Q ss_pred             CCCCCCCCCCC---------------------------------------------------------------------
Q psy6490         233 DPKHATPKNRP---------------------------------------------------------------------  243 (398)
Q Consensus       233 ~v~~~~~~~~~---------------------------------------------------------------------  243 (398)
                      .|.++......                                                                     
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            99877553310                                                                     


Q ss_pred             ---------------------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeec
Q psy6490         244 ---------------------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD  284 (398)
Q Consensus       244 ---------------------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~  284 (398)
                                                             ......++|||+||+.++++++|+++|++||.|++|+|+.+
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~  242 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG  242 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC
Confidence                                                   11224577999999999999999999999999999999866


Q ss_pred             CCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC-CEEEEEEecC
Q psy6490         285 QQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK-NKKVECKKAQ  326 (398)
Q Consensus       285 ~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~-g~~i~v~~a~  326 (398)
                      +     +|||||+|.+.++|.+++ .|||..|+ |+.|+|.|++
T Consensus       243 ~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          243 R-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             C-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            3     689999999987776665 59999999 9999999986

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

Probab=99.97  E-value=2.7e-31  Score=237.52  Aligned_cols=161  Identities=19%  Similarity=0.303  Sum_probs=140.6

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         158 DPTSAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       158 ~~~~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ..++++|||+|||. ++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|++|++ +++..+.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34789999999999 99999999999999999999999885     8899999999999999997 89999999999998


Q ss_pred             CCCCCCCC--------------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcC-CeeEEEEe
Q psy6490         236 HATPKNRP--------------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVML  282 (398)
Q Consensus       236 ~~~~~~~~--------------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G-~i~~v~i~  282 (398)
                      ++......                                ......++|||+|||.++++++|+++|++|| .|.+|+++
T Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~  185 (229)
T 2adc_A          106 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF  185 (229)
T ss_dssp             CCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC
T ss_pred             EecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEE
Confidence            87644110                                0012357899999999999999999999999 99999987


Q ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC-CEEEEEEecCch
Q psy6490         283 MDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK-NKKVECKKAQPK  328 (398)
Q Consensus       283 ~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~-g~~i~v~~a~~k  328 (398)
                      .+     ++|||||+|++.++|.+++ .|||..|+ |+.|+|.|++++
T Consensus       186 ~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          186 QK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             SS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            54     2789999999987776665 59999999 999999999764

>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=99.97  E-value=8.2e-31  Score=242.20  Aligned_cols=173  Identities=12%  Similarity=0.296  Sum_probs=151.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++|+++|+++|+.|| |.++++      ++++|||||+|.+.++|.+|++ +++..+.|+.|.+.+..
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            668999999999999999999999999 999988      3468999999999999999997 79999999999998754


Q ss_pred             CCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC
Q psy6490         239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN  317 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g  317 (398)
                               ..++|||+|||.++|+++|+++|+.||.|.+++++++..+|.++|||||+|.+.++|.+++ .|+|..|+|
T Consensus        94 ---------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g  164 (284)
T 3smz_A           94 ---------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP  164 (284)
T ss_dssp             ---------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             ---------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence                     3468999999999999999999999999999999999999999999999999988887766 799999999


Q ss_pred             EEEEEEecCchHHHhhhhhcCCccccCCCCCC
Q psy6490         318 KKVECKKAQPKEAVQANLLVGKRVILGPLGLR  349 (398)
Q Consensus       318 ~~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~  349 (398)
                      +.|+|.|+.++..... ....+.++++++...
T Consensus       165 ~~i~v~~a~~~~~~~~-~~~~~~l~v~nlp~~  195 (284)
T 3smz_A          165 RTLYVHWTDAGQLTPA-LLHSRCLCVDRLPPG  195 (284)
T ss_dssp             EECEEEECCGGGCCTT-TTSCSEEEEECCCTT
T ss_pred             cEEEEEECCCCCCCcc-cCCccEEEEecCCcc
Confidence            9999999988764322 234455566555443

>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=99.97  E-value=7.5e-31  Score=243.43  Aligned_cols=179  Identities=13%  Similarity=0.196  Sum_probs=144.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ..+...++|||+|||.++|+++|+++|+.||.|.+|+++++..+  ++|||||+|.+.++|.+|+++++..++|+.|.+.
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVS  113 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEE
Confidence            34457899999999999999999999999999999999998743  5899999999999999999999999999999998


Q ss_pred             CCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCc
Q psy6490         236 HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFH  313 (398)
Q Consensus       236 ~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G-~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~  313 (398)
                      +.          ..++|||+|||.++++++|+++|+.|| .|.+|+++++.. +.++|||||+|.+.++|.++++ |||.
T Consensus       114 ~~----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~  182 (292)
T 2ghp_A          114 HL----------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGL  182 (292)
T ss_dssp             EC----------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EC----------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            75          367899999999999999999999999 999999998864 8899999999999888877775 9999


Q ss_pred             eeCCEEEEEEecCchHHHhhh---hhcCCccccCCCC
Q psy6490         314 MIKNKKVECKKAQPKEAVQAN---LLVGKRVILGPLG  347 (398)
Q Consensus       314 ~i~g~~i~v~~a~~k~~~~~~---~~~~~~~~~~~~~  347 (398)
                      .|+|+.|+|.|+.++......   ...++.++++++.
T Consensus       183 ~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp  219 (292)
T 2ghp_A          183 KIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLS  219 (292)
T ss_dssp             EETTEECEEEECCCC---------CCTTTEEEEEEEC
T ss_pred             EeCCcEEEEEECCCCcccccccccCCCCceEEEECCC
Confidence            999999999999887654432   1333455665543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=4.5e-31  Score=230.79  Aligned_cols=159  Identities=19%  Similarity=0.307  Sum_probs=139.2

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+++|||+|||. ++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++ +++..++|+.|.|.++
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            468999999999 99999999999999999999999875     8899999999999999998 8999999999999877


Q ss_pred             CCCCCC--------------------------------ccCccccceeecCCCCCCCHHHHHHHHhhcC-CeeEEEEeec
Q psy6490         238 TPKNRP--------------------------------KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVMLMD  284 (398)
Q Consensus       238 ~~~~~~--------------------------------~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G-~i~~v~i~~~  284 (398)
                      ......                                ......++|||+|||.++++++|+++|++|| .|.+|+++.+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence            643210                                0112367899999999999999999999999 9999998765


Q ss_pred             CCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC-CEEEEEEecCch
Q psy6490         285 QQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK-NKKVECKKAQPK  328 (398)
Q Consensus       285 ~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~-g~~i~v~~a~~k  328 (398)
                      .     +|||||+|.+.++|.+++ .|||..|+ |+.|+|.|++++
T Consensus       157 ~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 D-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             T-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             C-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            2     789999999988776666 59999999 999999998764

>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=99.97  E-value=2.6e-30  Score=235.75  Aligned_cols=156  Identities=26%  Similarity=0.405  Sum_probs=141.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++.++      +|||||+|.+.++|.+|++ +++..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            347789999999999999999999999999999999654      8999999999999999998 899999999999998


Q ss_pred             CCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HH-CCce
Q psy6490         237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EI-HFHM  314 (398)
Q Consensus       237 ~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l-~~~~  314 (398)
                      +..         .++|||+|||.++|+++|+++|+.||.|.+|+|++| .+|+++|||||+|.+.++|.+|+ .| ++..
T Consensus        93 a~~---------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~  162 (261)
T 3sde_A           93 ATH---------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAF  162 (261)
T ss_dssp             CCC---------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCE
T ss_pred             ccc---------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeE
Confidence            863         467999999999999999999999999999999999 68999999999999987776665 57 5666


Q ss_pred             eC---CEEEEEEecCchH
Q psy6490         315 IK---NKKVECKKAQPKE  329 (398)
Q Consensus       315 i~---g~~i~v~~a~~k~  329 (398)
                      +.   ++.|.|.++....
T Consensus       163 ~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          163 LLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             ESSSSCCBCEEEECCCEE
T ss_pred             EecCCCceEEEeeccccC
Confidence            65   9999999998764

>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=99.91  E-value=4.8e-24  Score=179.17  Aligned_cols=138  Identities=17%  Similarity=0.263  Sum_probs=107.5

Q ss_pred             EEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCc-ccCC------cccCCCCC---CCCCCCccCccccceeecCCC
Q psy6490         190 DVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIH-TLDG------KKIDPKHA---TPKNRPKIGNRTKKIFVGGVS  258 (398)
Q Consensus       190 ~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~-~~~g------~~l~v~~~---~~~~~~~~~~~~~~l~V~nLp  258 (398)
                      .++++.+..  +++|||||+|.+.++|++|++ +++. .++|      ........   ............++|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            456777643  589999999999999999996 3322 1222      11111111   111122233457899999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchH
Q psy6490         259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       259 ~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      +++|+++|+++|+.||.|++|+|++|+.+++++|||||+|.+.++|++++ .|||..|+|+.|+|.|++++.
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999999999999999999999989999999999999988887766 599999999999999998764

>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=99.87  E-value=2.4e-22  Score=167.20  Aligned_cols=123  Identities=20%  Similarity=0.278  Sum_probs=106.9

Q ss_pred             CCcccEEEEEEcChHhHHHHHh-C-CCcccCCcccCCCCCCCC-------------CCCccCccccceeecCCCCCCCHH
Q psy6490         200 QRSRGFGFITFAEPETVEKVLK-V-PIHTLDGKKIDPKHATPK-------------NRPKIGNRTKKIFVGGVSQDTSAE  264 (398)
Q Consensus       200 ~~~~g~afV~f~~~e~a~~al~-~-~~~~~~g~~l~v~~~~~~-------------~~~~~~~~~~~l~V~nLp~~~tee  264 (398)
                      ...+|+++|+|.+.++|++|++ + ++..++| .|.+.++..+             .........++|||+|||+++|++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            4579999999999999999997 7 8999999 8888877642             223334567899999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         265 EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       265 ~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      +|+++|+.||.|++|+|+++     ++|||||+|.+.++|++++ .|||..|+|+.|+|+|+.++
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            99999999999999999877     5899999999988777766 59999999999999999875

>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=99.86  E-value=2.4e-22  Score=159.25  Aligned_cols=104  Identities=16%  Similarity=0.375  Sum_probs=73.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++|+++|+++|++||.|.+|+|++|+  +.+||||||+|.+.++|++||+ +++..++|+.|.|.++.
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 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999985  4589999999999999999997 89999999999999887


Q ss_pred             CCCCCc-----cCccccceeecCCCCCCCHHH
Q psy6490         239 PKNRPK-----IGNRTKKIFVGGVSQDTSAEE  265 (398)
Q Consensus       239 ~~~~~~-----~~~~~~~l~V~nLp~~~tee~  265 (398)
                      .+....     .....++|||+||+.++|++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC----------------------------
T ss_pred             CccccccccccccCCCCceEeCCCCCCccccc
Confidence            654322     223445799999999999874

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.86  E-value=2.1e-21  Score=149.25  Aligned_cols=80  Identities=20%  Similarity=0.440  Sum_probs=74.7

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++|+++|+++|++||.|++|+|++|+.+|+++|||||+|.+.++|++|+ .|||..|+|+.|+|+||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4568999999999999999999999999999999999999999999999999988776666 699999999999999997


Q ss_pred             c
Q psy6490         327 P  327 (398)
Q Consensus       327 ~  327 (398)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

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

Probab=99.84  E-value=1.1e-20  Score=147.96  Aligned_cols=87  Identities=15%  Similarity=0.284  Sum_probs=79.8

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+||++++++++|+++|++||.|++|+|++|+.+++++|||||+|++.++|++|+ +|||..|+|+.|+|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4678999999999999999999999999999999999999999999999999988777666 699999999999999998


Q ss_pred             chHHHhhh
Q psy6490         327 PKEAVQAN  334 (398)
Q Consensus       327 ~k~~~~~~  334 (398)
                      .+..+++.
T Consensus        85 ~~~~~~~~   92 (110)
T 3s8s_A           85 KGQQRMKY   92 (110)
T ss_dssp             TTHHHHHH
T ss_pred             CCcHHHHH
Confidence            87766653

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.83  E-value=5.7e-21  Score=144.56  Aligned_cols=82  Identities=20%  Similarity=0.377  Sum_probs=74.9

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-H-CCceeCCEEEEEEec
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I-HFHMIKNKKVECKKA  325 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G-~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l-~~~~i~g~~i~v~~a  325 (398)
                      +++|||+|||.++||++|+++|++|| .|++|+|++|+.++.+||||||+|.+.++|++|++ + ++..|+|+.|+|+|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999999999999999999999999988888875 4 567899999999999


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            88754

>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=99.82  E-value=2.4e-20  Score=143.32  Aligned_cols=80  Identities=24%  Similarity=0.470  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            56899999999999999999999999999999999999999999999999999999999997 89999999999999886


Q ss_pred             C
Q psy6490         239 P  239 (398)
Q Consensus       239 ~  239 (398)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=3.3e-20  Score=142.89  Aligned_cols=86  Identities=47%  Similarity=0.915  Sum_probs=80.1

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||.++++++|+++|+.||.|++|+|++++.+++++|||||+|++.++|+++++||+..|+|+.|+|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34678999999999999999999999999999999999999999999999999999999888889999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      .++..+
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            887543

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

Probab=99.81  E-value=2.6e-20  Score=141.61  Aligned_cols=81  Identities=19%  Similarity=0.359  Sum_probs=72.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCC--eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCc----eeCCEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGK--VEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFH----MIKNKK  319 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~--i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~----~i~g~~  319 (398)
                      ..-.+|||+|||+++|+|+|+++|++||.  |.+|++++|+.+|++||||||+|.+.++|++++ .|||.    .|+||.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            45678999999999999999999999995  678999999999999999999999977776655 68886    599999


Q ss_pred             EEEEecCc
Q psy6490         320 VECKKAQP  327 (398)
Q Consensus       320 i~v~~a~~  327 (398)
                      |+|+||+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999974

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.81  E-value=1.1e-19  Score=135.13  Aligned_cols=80  Identities=21%  Similarity=0.390  Sum_probs=75.0

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      .+|||+|||.++++++|+++|+.||.|.++.++++..++.++|||||+|.+.++|++++ .|||..|+|+.|+|+|+.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            57999999999999999999999999999999999999999999999999988887776 49999999999999999876


Q ss_pred             H
Q psy6490         329 E  329 (398)
Q Consensus       329 ~  329 (398)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.81  E-value=1.2e-19  Score=136.20  Aligned_cols=82  Identities=22%  Similarity=0.454  Sum_probs=73.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++++ .|||..|+|+.|+|+|+
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            35678999999999999999999999999999999999889999999999999988777766 59999999999999999


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>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=99.81  E-value=1.2e-19  Score=136.10  Aligned_cols=80  Identities=38%  Similarity=0.704  Sum_probs=75.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++++++++..|+|+.|+|++|
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999986

>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=99.81  E-value=1.3e-19  Score=143.59  Aligned_cols=87  Identities=21%  Similarity=0.382  Sum_probs=79.1

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++++ .||+..|+|+.|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3446689999999999999999999999999999999999989999999999999988777666 799999999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |++++..+
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpz_A          101 LKRSKNDS  108 (115)
T ss_dssp             CCCCSCCC
T ss_pred             EcCCCCcC
Confidence            99887543

>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=99.81  E-value=8e-20  Score=144.66  Aligned_cols=83  Identities=20%  Similarity=0.467  Sum_probs=72.8

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..+|||+|||+++|+++|+++|++||.|++|+|++|.  +.+||||||+|++.++|++|+ +||+..|+|+.|+|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4679999999999999999999999999999999995  458999999999988887666 6999999999999999988


Q ss_pred             hHHHhh
Q psy6490         328 KEAVQA  333 (398)
Q Consensus       328 k~~~~~  333 (398)
                      +..+..
T Consensus        83 ~~~~~~   88 (115)
T 4f25_A           83 RKEREA   88 (115)
T ss_dssp             CCC---
T ss_pred             cccccc
Confidence            765543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.81  E-value=2.9e-19  Score=146.51  Aligned_cols=84  Identities=21%  Similarity=0.391  Sum_probs=79.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|+.||.|++|++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  120 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            67999999999999999999999999999999999999999999999999999999999998 89999999999999988


Q ss_pred             CCCCC
Q psy6490         239 PKNRP  243 (398)
Q Consensus       239 ~~~~~  243 (398)
                      .+...
T Consensus       121 ~~~~~  125 (139)
T 1u6f_A          121 SGHQR  125 (139)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

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

Probab=99.81  E-value=2.7e-20  Score=151.57  Aligned_cols=121  Identities=15%  Similarity=0.215  Sum_probs=80.2

Q ss_pred             EEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEee
Q psy6490         205 FGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM  283 (398)
Q Consensus       205 ~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~  283 (398)
                      +.|++|.+...+..|+. +++....|+.- ..+..   ........++|||+|||.++|+++|+++|++||.|++|+|++
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~---~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   81 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGR---PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR   81 (135)
T ss_dssp             ------------------------------CCSCC---SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCC
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcCC---CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            67888888888888887 55544444431 12222   233445678999999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchH
Q psy6490         284 DQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       284 ~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      ++.+++++|||||+|++.++|++++ .||+..|+|+.|+|+|++++.
T Consensus        82 ~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             CSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9889999999999999988887777 599999999999999998754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.9e-19  Score=135.66  Aligned_cols=84  Identities=23%  Similarity=0.379  Sum_probs=77.0

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ......++|||+|||.++++++|+++|++||.|++|.+++++.+++++|||||+|.+.++|++++ .||+..|+|+.|+|
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            34556789999999999999999999999999999999999999999999999999988877766 59999999999999


Q ss_pred             EecCc
Q psy6490         323 KKAQP  327 (398)
Q Consensus       323 ~~a~~  327 (398)
                      +|+++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

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

Probab=99.80  E-value=1.5e-19  Score=140.15  Aligned_cols=85  Identities=14%  Similarity=0.356  Sum_probs=78.2

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      .....++|||+|||.++++++|+++|+.|| |.+|+|++++.+++++|||||+|++.++|+++++||+..|+|+.|+|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDI   89 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEE
Confidence            345678999999999999999999999997 9999999999999999999999999888877779999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=3.4e-19  Score=141.12  Aligned_cols=90  Identities=23%  Similarity=0.445  Sum_probs=80.9

Q ss_pred             CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       243 ~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      .......++|||+|||.++++++|+++|+.||.|++|+|++++.++.++|||||+|.+.++|++|+ .||+..|+|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            344556789999999999999999999999999999999999889999999999999988887776 5999999999999


Q ss_pred             EEecCchHHHh
Q psy6490         322 CKKAQPKEAVQ  332 (398)
Q Consensus       322 v~~a~~k~~~~  332 (398)
                      |.|++++....
T Consensus        89 V~~a~~~~~~~   99 (115)
T 2dgo_A           89 TNWATRKPPAP   99 (115)
T ss_dssp             EEESSCCCCCS
T ss_pred             EEEccCCCCCC
Confidence            99998876543

>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=99.80  E-value=1e-19  Score=147.61  Aligned_cols=86  Identities=17%  Similarity=0.234  Sum_probs=78.9

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGK---VEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~---i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v  322 (398)
                      ....++|||+|||+++|+++|+++|+.||.   |++|+|++|+. |+++|||||+|++.++|++|+++|+..|+||.|+|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            345678999999999999999999999999   89999999976 99999999999999999888889999999999999


Q ss_pred             EecCchHHHh
Q psy6490         323 KKAQPKEAVQ  332 (398)
Q Consensus       323 ~~a~~k~~~~  332 (398)
                      .++..++...
T Consensus       120 ~~a~~~e~~~  129 (136)
T 2hgl_A          120 FKSHRTEMDW  129 (136)
T ss_dssp             EECCHHHHHH
T ss_pred             EECChHHHHH
Confidence            9998877554

>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=99.80  E-value=1.8e-19  Score=138.76  Aligned_cols=86  Identities=24%  Similarity=0.406  Sum_probs=78.9

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|+.||.|++|+|++++.+++++|||||+|.+.++|++++ .||+..|+|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999999999889999999999999988887766 7999999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9887654

>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=6e-20  Score=147.56  Aligned_cols=82  Identities=17%  Similarity=0.450  Sum_probs=76.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||.++|+++|+++|+.||.|++|+|++++.++.++|||||+|.+.++|+++++|||..|+|+.|+|.|++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            35678999999999999999999999999999999999989999999999999988888777999999999999999997


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      +.
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.80  E-value=1.2e-19  Score=143.49  Aligned_cols=86  Identities=15%  Similarity=0.329  Sum_probs=79.1

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||.++++++|+++|+.||.|++|+|++|+.++.++|||||+|.+.++|+++++||+..|+|+.|+|.|+.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecC
Confidence            45678999999999999999999999999999999999999999999999999988777666999999999999999998


Q ss_pred             chHHHh
Q psy6490         327 PKEAVQ  332 (398)
Q Consensus       327 ~k~~~~  332 (398)
                      ++..+.
T Consensus       103 ~~~~~~  108 (114)
T 2cq4_A          103 AEKNRL  108 (114)
T ss_dssp             HHHHHH
T ss_pred             CCccCC
Confidence            876654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.5e-19  Score=140.16  Aligned_cols=86  Identities=20%  Similarity=0.354  Sum_probs=78.8

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|.|++++.++.++|||||+|.+.++|++|+ .||+..|+|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            3456789999999999999999999999999999999999989999999999999988887766 599999999999999


Q ss_pred             ecCchHH
Q psy6490         324 KAQPKEA  330 (398)
Q Consensus       324 ~a~~k~~  330 (398)
                      |+.++..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987753

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.80  E-value=2.5e-19  Score=133.81  Aligned_cols=80  Identities=24%  Similarity=0.500  Sum_probs=74.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|.++++..+++++|||||+|.+.++|++++ .|||..|+|+.|+|+|+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45788999999999999999999999999999999999899999999999999988887766 79999999999999998


Q ss_pred             C
Q psy6490         326 Q  326 (398)
Q Consensus       326 ~  326 (398)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1e-19  Score=140.69  Aligned_cols=85  Identities=18%  Similarity=0.262  Sum_probs=77.9

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|++|.. +.++|||||+|++.++|++|+++++..|+|+.|+|.|+.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            4568999999999999999999999999999999999976 999999999999999999988899999999999999987


Q ss_pred             chHHHh
Q psy6490         327 PKEAVQ  332 (398)
Q Consensus       327 ~k~~~~  332 (398)
                      .....+
T Consensus        88 ~~~~~k   93 (103)
T 1s79_A           88 DYFAKK   93 (103)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            754443

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.80  E-value=3.1e-19  Score=136.52  Aligned_cols=85  Identities=19%  Similarity=0.411  Sum_probs=78.0

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      +++|||+|||.++++++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|++++ .|||..|+|+.|+|+|+.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            578999999999999999999999999999999999999999999999999988777666 6999999999999999998


Q ss_pred             hHHHhh
Q psy6490         328 KEAVQA  333 (398)
Q Consensus       328 k~~~~~  333 (398)
                      +.....
T Consensus        82 ~~~~~~   87 (96)
T 2x1f_A           82 SDISGV   87 (96)
T ss_dssp             SSGGGH
T ss_pred             CCCCCc
Confidence            765543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.80  E-value=1.4e-19  Score=141.77  Aligned_cols=86  Identities=41%  Similarity=0.710  Sum_probs=76.7

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|+++++..+..|+|+.|+|++
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~  100 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV  100 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999988888778999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +.++..
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987754

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

Probab=99.80  E-value=1.8e-19  Score=140.60  Aligned_cols=85  Identities=14%  Similarity=0.311  Sum_probs=77.7

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|++++ .|||..|+|+.|+|+
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            3446788999999999999999999999999999999999999999999999999988877766 599999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |+.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998753

>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=99.80  E-value=2.5e-19  Score=135.05  Aligned_cols=81  Identities=22%  Similarity=0.481  Sum_probs=75.8

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..++|||+|||.++++++|+++|+.||.|.++++.++..+++++|||||+|.+.++|++++++|+..|+|+.|+|.++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            45789999999999999999999999999999999998899999999999999888877779999999999999999976


Q ss_pred             h
Q psy6490         328 K  328 (398)
Q Consensus       328 k  328 (398)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=2.3e-19  Score=137.03  Aligned_cols=84  Identities=19%  Similarity=0.493  Sum_probs=77.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|++.++|++++ .||+..|+|+.|+|+|+
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            35688999999999999999999999999999999999999999999999999988887766 59999999999999999


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1e-19  Score=139.18  Aligned_cols=85  Identities=21%  Similarity=0.409  Sum_probs=78.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEe
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET-VMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKK  324 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v-~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~  324 (398)
                      ...++|||+|||.++++++|+++|++||.|.+| +|++|+.++.++|||||+|++.++|+++++ ||+..|+|+.|+|+|
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            356889999999999999999999999999999 999998899999999999999888877776 999999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +.++..+
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9877543

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

Probab=99.79  E-value=4.3e-19  Score=136.82  Aligned_cols=84  Identities=17%  Similarity=0.366  Sum_probs=76.8

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++++ .||+..|+|+.|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567889999999999999999999999999999999997 8999999999999988887766 799999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |++++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.9e-19  Score=140.15  Aligned_cols=87  Identities=31%  Similarity=0.635  Sum_probs=79.9

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      .....++|||+|||.++++++|+++|+.||.|++|+|++++.++.++|||||+|++.++|+++++.++..|+|+.|+|++
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999888888776699999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +.++...
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9887643

>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=99.79  E-value=4.8e-19  Score=137.32  Aligned_cols=87  Identities=30%  Similarity=0.519  Sum_probs=79.3

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK  323 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~  323 (398)
                      ......++|||+|||.++++++|+++|+.||.|++|+|++++.+++++|||||+|++.++|+++++ ++..|+|+.|+|+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~   88 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEE
Confidence            344567889999999999999999999999999999999999999999999999999999988887 6889999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |+.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99887543

>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=7.1e-20  Score=133.36  Aligned_cols=75  Identities=64%  Similarity=1.185  Sum_probs=72.3

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      +|||+|||.++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++++++|+..|+|+.|+|+||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            589999999999999999999999999999999988999999999999999999999999999999999999986

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.79  E-value=3e-19  Score=139.60  Aligned_cols=87  Identities=20%  Similarity=0.493  Sum_probs=79.1

Q ss_pred             CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       243 ~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      .......++|||+|||.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++++ .|||..|+|+.|+
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            344556789999999999999999999999999999999999999999999999999988887766 5999999999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |++++++.
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

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.79  E-value=6.6e-20  Score=138.52  Aligned_cols=82  Identities=12%  Similarity=0.242  Sum_probs=70.1

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G--~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      .+|||+|||+++|+++|+++|++||  .|.+|++++|+.+|+++|||||+|.+.++|++|+ .|||..|+|+.|+|.++.
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  9999999999999999999999999988887776 699999999999999998


Q ss_pred             chHHH
Q psy6490         327 PKEAV  331 (398)
Q Consensus       327 ~k~~~  331 (398)
                      ++...
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76543

>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=3.4e-19  Score=140.81  Aligned_cols=88  Identities=10%  Similarity=0.158  Sum_probs=81.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCe-eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV-EETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i-~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||+++|+++|+++|+.||.| .+|+|++|+ +++++|||||+|++.++|++|+++|+..|+|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            4456889999999999999999999999999 899999997 99999999999999999999888899999999999999


Q ss_pred             cCchHHHhhh
Q psy6490         325 AQPKEAVQAN  334 (398)
Q Consensus       325 a~~k~~~~~~  334 (398)
                      +.+++.+...
T Consensus        91 a~~~~~~~~~  100 (114)
T 2cpy_A           91 VTLEDMREIE  100 (114)
T ss_dssp             ECHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            9998876654

>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=99.79  E-value=2.1e-19  Score=139.64  Aligned_cols=86  Identities=17%  Similarity=0.378  Sum_probs=78.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT-KRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~-~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||+++++++|+++|+.|| |.+|.|++++.+ ++++|||||+|.+.++|+++++||+..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVD   89 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEE
Confidence            345678999999999999999999999999 999999999887 999999999999988887777999999999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      ++.++..+
T Consensus        90 ~a~~~~~~   97 (104)
T 1wi8_A           90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99887543

>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=99.79  E-value=3.4e-19  Score=140.16  Aligned_cols=88  Identities=16%  Similarity=0.307  Sum_probs=79.4

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHC------CceeC
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIH------FHMIK  316 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~------~~~i~  316 (398)
                      ......++|||+|||+++++++|+++|+.||.|.+|+|++|+.++.++|||||+|.+.++|++++ .||      +..|+
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            34456789999999999999999999999999999999999999999999999999988777766 588      99999


Q ss_pred             CEEEEEEecCchHHH
Q psy6490         317 NKKVECKKAQPKEAV  331 (398)
Q Consensus       317 g~~i~v~~a~~k~~~  331 (398)
                      |+.|+|.|+.++...
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999887544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=1e-19  Score=140.27  Aligned_cols=85  Identities=20%  Similarity=0.257  Sum_probs=77.9

Q ss_pred             cccceeecCCCC------CCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC-EE
Q psy6490         248 RTKKIFVGGVSQ------DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN-KK  319 (398)
Q Consensus       248 ~~~~l~V~nLp~------~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g-~~  319 (398)
                      ..++|||+|||.      ++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|+ .|||..|+| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467899999999      9999999999999999999999999999999999999999988777666 699999999 99


Q ss_pred             EEEEecCchHHHh
Q psy6490         320 VECKKAQPKEAVQ  332 (398)
Q Consensus       320 i~v~~a~~k~~~~  332 (398)
                      |+|.++.+++...
T Consensus        85 l~V~~a~~~~~~~   97 (100)
T 3ns6_A           85 LFLYTMKDVERYN   97 (100)
T ss_dssp             CEEEESHHHHHHH
T ss_pred             EEEEECchhhhhh
Confidence            9999998876543

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

Probab=99.79  E-value=5.1e-19  Score=140.78  Aligned_cols=83  Identities=20%  Similarity=0.390  Sum_probs=75.2

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ......++|||+|||+++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++++ .|||..|+|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999999999999999999987776666 59999999999999


Q ss_pred             EecC
Q psy6490         323 KKAQ  326 (398)
Q Consensus       323 ~~a~  326 (398)
                      +|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9974

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=4.4e-20  Score=139.64  Aligned_cols=83  Identities=19%  Similarity=0.367  Sum_probs=76.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C-CCcccCCcccCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V-PIHTLDGKKIDPKHA  237 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~-~~~~~~g~~l~v~~~  237 (398)
                      +++|||+|||.++|+++|+++|++|| .|.+|++++|+.+|.++|||||+|.+.++|++|++ + ++..++|++|.|.++
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            47999999999999999999999999 89999999999999999999999999999999998 4 456799999999999


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876553

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

Probab=99.79  E-value=2.1e-19  Score=142.55  Aligned_cols=87  Identities=37%  Similarity=0.643  Sum_probs=80.2

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      .....++|||+|||.++++++|+++|+.||.|++|+|++++.++.++|||||+|.+.++|+++++.++..|+|+.|+|.|
T Consensus        23 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEEC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999988887799999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +.++...
T Consensus       103 a~~~~~~  109 (116)
T 1x4b_A          103 AVAREES  109 (116)
T ss_dssp             CSSCCCC
T ss_pred             CCCCccC
Confidence            9887643

>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=99.79  E-value=3.5e-19  Score=139.89  Aligned_cols=85  Identities=14%  Similarity=0.287  Sum_probs=77.8

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|++++ .|||..|+|+.|+|.
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            3456789999999999999999999999999999999999999999999999999988777766 599999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |+.++.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            998764

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=7.7e-19  Score=133.77  Aligned_cols=81  Identities=16%  Similarity=0.395  Sum_probs=75.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|++||.|.+|++++++.++.++|||||+|++.++|++++ .||+..|+|+.|+|+|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            446789999999999999999999999999999999999999999999999999988887766 6999999999999999


Q ss_pred             cC
Q psy6490         325 AQ  326 (398)
Q Consensus       325 a~  326 (398)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>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=99.79  E-value=2.3e-19  Score=139.70  Aligned_cols=86  Identities=29%  Similarity=0.442  Sum_probs=78.6

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|.|++++.++.++|||||+|.+.++|+++++ ||+..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999888877765 89999999999999


Q ss_pred             ecCchHH
Q psy6490         324 KAQPKEA  330 (398)
Q Consensus       324 ~a~~k~~  330 (398)
                      |+.++..
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9987653

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.3e-19  Score=138.88  Aligned_cols=86  Identities=23%  Similarity=0.483  Sum_probs=78.7

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|+.||.|++|+|++++.+++++|||||+|.+.++|++|+ .||+..|+|+.|+|.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            446789999999999999999999999999999999999999999999999999988887766 6999999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      ++++..+
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9877543

>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=99.79  E-value=4.1e-19  Score=149.96  Aligned_cols=88  Identities=14%  Similarity=0.287  Sum_probs=76.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||..+++++|+++|+.||.|..|.|++++.+|.++|||||+|.+.++|++|+ .|||..|+|+.|+|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345678999999999999999999999999999999999999999999999999988777666 5999999999999999


Q ss_pred             cCchHHHhh
Q psy6490         325 AQPKEAVQA  333 (398)
Q Consensus       325 a~~k~~~~~  333 (398)
                      +.++..+..
T Consensus       149 a~~~~~~~~  157 (165)
T 1rk8_A          149 CFVKGPKRV  157 (165)
T ss_dssp             SEECC----
T ss_pred             ecCCCCCCC
Confidence            988765543

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

Probab=99.79  E-value=2.8e-19  Score=140.07  Aligned_cols=82  Identities=16%  Similarity=0.263  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+||+.++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|++ +|+..++|+.|.|.++
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            367899999999999999999999999999999999999999999999999999999999998 8999999999999887


Q ss_pred             CCC
Q psy6490         238 TPK  240 (398)
Q Consensus       238 ~~~  240 (398)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=2.3e-19  Score=137.87  Aligned_cols=84  Identities=19%  Similarity=0.399  Sum_probs=75.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ---TKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVEC  322 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~---~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v  322 (398)
                      ...++|||+|||.++++++|+++|++||.|++|.|+++..   ++.++|||||+|.+.++|+++++ ||+..|+|+.|+|
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            3568899999999999999999999999999999999876   66899999999999888877665 8999999999999


Q ss_pred             EecCchHH
Q psy6490         323 KKAQPKEA  330 (398)
Q Consensus       323 ~~a~~k~~  330 (398)
                      +|+.++..
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99987653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.8e-19  Score=139.74  Aligned_cols=85  Identities=18%  Similarity=0.312  Sum_probs=77.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|++|+ .||+..|+|+.|+|.
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            3456789999999999999999999999999999999999999999999999999987777666 599999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |++.+.
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            998654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=8.2e-19  Score=134.99  Aligned_cols=86  Identities=41%  Similarity=0.794  Sum_probs=80.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|+++++..++|+.|.|.++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34779999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876553

>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=99.79  E-value=2.5e-19  Score=139.22  Aligned_cols=88  Identities=18%  Similarity=0.423  Sum_probs=80.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|.+++++.++.++|||||+|.+.++|++++ .|||..|+|+.|+|+|+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            45689999999999999999999999999999999999989999999999999988887777 59999999999999999


Q ss_pred             CchHHHhhh
Q psy6490         326 QPKEAVQAN  334 (398)
Q Consensus       326 ~~k~~~~~~  334 (398)
                      .++..+...
T Consensus        86 ~~~~~~~~~   94 (104)
T 1p1t_A           86 ASEKNKEEL   94 (104)
T ss_dssp             TCTTHHHHH
T ss_pred             CCccchhhh
Confidence            988776654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=3.4e-19  Score=138.17  Aligned_cols=87  Identities=25%  Similarity=0.441  Sum_probs=77.9

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ......++|||+|||.++|+++|+++|++||.|.+|.|+++  ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|
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            34456789999999999999999999999999999999998  8999999999999988777766 59999999999999


Q ss_pred             EecCchHHHh
Q psy6490         323 KKAQPKEAVQ  332 (398)
Q Consensus       323 ~~a~~k~~~~  332 (398)
                      .|+.++..+.
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2d9p_A           88 ALAQRKEERQ   97 (103)
T ss_dssp             EECSSCCCCC
T ss_pred             EEecccccCC
Confidence            9998876543

>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=4.9e-19  Score=140.69  Aligned_cols=87  Identities=20%  Similarity=0.260  Sum_probs=79.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGK---VEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~---i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v  322 (398)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|++++. |+++|||||+|++.++|++|+++|+..|+||.|+|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            345678999999999999999999999999   89999999976 99999999999999999888889999999999999


Q ss_pred             EecCchHHHhh
Q psy6490         323 KKAQPKEAVQA  333 (398)
Q Consensus       323 ~~a~~k~~~~~  333 (398)
                      .++..++....
T Consensus        93 ~~a~~~~~~~~  103 (118)
T 2db1_A           93 FKSHRTEMDWV  103 (118)
T ss_dssp             EEECHHHHHHH
T ss_pred             EECCHHHHHHH
Confidence            99988775543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.3e-19  Score=138.92  Aligned_cols=85  Identities=32%  Similarity=0.612  Sum_probs=78.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|+.||.|++|+|++++.++.++|||||+|.+.++|++++ .||+..|+|+.|+|.|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            446789999999999999999999999999999999999999999999999999988877766 7999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      ++++..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.5e-18  Score=137.67  Aligned_cols=92  Identities=34%  Similarity=0.625  Sum_probs=81.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      ...+...++|||+|||.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++ +++ .|+|+.|.
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            3445578999999999999999999999999999999999999999999999999999999999999 555 89999999


Q ss_pred             CCCCCCCCCCccCc
Q psy6490         234 PKHATPKNRPKIGN  247 (398)
Q Consensus       234 v~~~~~~~~~~~~~  247 (398)
                      |.++..........
T Consensus        90 V~~a~~~~~~~~~~  103 (116)
T 2cqd_A           90 VNLAYLGAKPRSLQ  103 (116)
T ss_dssp             EEESTTTCCCCCCC
T ss_pred             EEEcccCCCccccC
Confidence            99997765544433

>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=99.78  E-value=4.7e-19  Score=142.99  Aligned_cols=85  Identities=24%  Similarity=0.377  Sum_probs=77.8

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|+|++|+.+++++|||||+|++.++|++|+ +|||..|+|+.|+|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999999999999999999999988777766 599999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |+.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            998763

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.78  E-value=8.6e-19  Score=134.85  Aligned_cols=82  Identities=20%  Similarity=0.331  Sum_probs=75.3

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE--------TVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI  315 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~--------v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i  315 (398)
                      .....++|||+|||.++++++|+++|++||.|.+        |++++|+.+++++|||||+|.+.++|++++ .|||..|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3446789999999999999999999999999999        999999999999999999999988887766 5999999


Q ss_pred             CCEEEEEEecC
Q psy6490         316 KNKKVECKKAQ  326 (398)
Q Consensus       316 ~g~~i~v~~a~  326 (398)
                      +|+.|+|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999974

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=6.5e-19  Score=144.44  Aligned_cols=87  Identities=18%  Similarity=0.394  Sum_probs=79.2

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|++.++|++|+ +||+..|+|+.|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999999999999999999999988887766 599999999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |++++..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99887544

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

Probab=99.78  E-value=1e-18  Score=145.63  Aligned_cols=86  Identities=19%  Similarity=0.293  Sum_probs=77.2

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G--~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ..++|||+||++++|+++|+++|+.||  .|.+|+|++|+.+|+++|||||+|.+.++|++|+ .|||..|+|+.|+|++
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            457899999999999999999999999  9999999999999999999999999988877766 5799999999999999


Q ss_pred             cCchHHHhh
Q psy6490         325 AQPKEAVQA  333 (398)
Q Consensus       325 a~~k~~~~~  333 (398)
                      +.++.....
T Consensus       134 a~~~~~~~~  142 (156)
T 3n9u_C          134 ATRQNLSQF  142 (156)
T ss_dssp             CCHHHHHHH
T ss_pred             cCCCcchhh
Confidence            988765443

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=133.24  Aligned_cols=82  Identities=18%  Similarity=0.346  Sum_probs=74.4

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|+|.+++. ++++|||||+|++.++|+++++ ||+..|+|+.|+|+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            345678999999999999999999999999999999999975 9999999999999887777765 99999999999999


Q ss_pred             ecCc
Q psy6490         324 KAQP  327 (398)
Q Consensus       324 ~a~~  327 (398)
                      |++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>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=99.78  E-value=6.1e-19  Score=137.25  Aligned_cols=86  Identities=24%  Similarity=0.403  Sum_probs=77.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC---EEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN---KKV  320 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g---~~i  320 (398)
                      .....++|||+|||.++++++|+++|+.||.|++|+|++++ ++.++|||||+|.+.++|++|+ .||+..|.|   +.|
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            34567899999999999999999999999999999999997 7999999999999988777766 599999998   999


Q ss_pred             EEEecCchHHH
Q psy6490         321 ECKKAQPKEAV  331 (398)
Q Consensus       321 ~v~~a~~k~~~  331 (398)
                      +|.|+.++..+
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999887654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=5.8e-19  Score=137.86  Aligned_cols=88  Identities=24%  Similarity=0.411  Sum_probs=78.9

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHH-HH-CCceeCCEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD-QQTKRHRGFGFVTFENEEVVDHIC-EI-HFHMIKNKKV  320 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~-~~~~~~kg~afV~F~~~eaa~a~~-~l-~~~~i~g~~i  320 (398)
                      ......++|||+|||.++++++|+++|+.||.|++|+|+++ +.++.++|||||+|.+.++|++|+ .| |+..|+|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34456789999999999999999999999999999999999 789999999999999988777666 68 9999999999


Q ss_pred             EEEecCchHHH
Q psy6490         321 ECKKAQPKEAV  331 (398)
Q Consensus       321 ~v~~a~~k~~~  331 (398)
                      +|.|+.++...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999887543

>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=99.78  E-value=1.4e-18  Score=135.19  Aligned_cols=87  Identities=30%  Similarity=0.502  Sum_probs=81.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .+....++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|
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            444578999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++..+..
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99887654

>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=99.78  E-value=5.5e-19  Score=132.52  Aligned_cols=81  Identities=54%  Similarity=0.938  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      .+...++|||+|||.++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|+++++..++|+.|.|++
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44578999999999999999999999999999999999999999999999999999999999999888899999998875


Q ss_pred             C
Q psy6490         237 A  237 (398)
Q Consensus       237 ~  237 (398)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.78  E-value=1.5e-18  Score=134.54  Aligned_cols=85  Identities=19%  Similarity=0.306  Sum_probs=75.3

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|+|+++..+  ++|||||+|.+.++|++|+ .||+..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            3456789999999999999999999999999999999998543  6899999999988887766 599999999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |++++..+
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqi_A           89 WATTPSSQ   96 (103)
T ss_dssp             ECCCTTCC
T ss_pred             ECCCCccc
Confidence            99886544

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.77  E-value=3.1e-19  Score=144.70  Aligned_cols=86  Identities=15%  Similarity=0.310  Sum_probs=76.4

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCc----eeCC
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE--TVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFH----MIKN  317 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~--v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~----~i~g  317 (398)
                      ......++|||+|||+++|+++|+++|++||.|..  |+|++|+.+|++||||||+|++.++.+++..|||.    .|+|
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHHHHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCHHHHHHHHHhcCCCCCccCCC
Confidence            33456789999999999999999999999999976  99999999999999999999999444555689999    9999


Q ss_pred             EEEEEEecCchH
Q psy6490         318 KKVECKKAQPKE  329 (398)
Q Consensus       318 ~~i~v~~a~~k~  329 (398)
                      |.|+|+|++++.
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999999998764

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.77  E-value=1.6e-18  Score=137.29  Aligned_cols=88  Identities=30%  Similarity=0.513  Sum_probs=81.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .+..+.++|||+|||.++++++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++|++ +++..|+|+.|.|
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            445578999999999999999999999999999999999999899999999999999999999998 8999999999999


Q ss_pred             CCCCCCCCC
Q psy6490         235 KHATPKNRP  243 (398)
Q Consensus       235 ~~~~~~~~~  243 (398)
                      .++..+...
T Consensus        90 ~~a~~~~~~   98 (115)
T 2dgo_A           90 NWATRKPPA   98 (115)
T ss_dssp             EESSCCCCC
T ss_pred             EEccCCCCC
Confidence            998876553

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=136.10  Aligned_cols=84  Identities=19%  Similarity=0.286  Sum_probs=76.5

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ....+|||+|||+++|++||+++|+.| .|.+|+|++|+. |+++|||||+|++.++|++|+++|+..|+||.|+|..+.
T Consensus        14 ~~~~~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           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            345789999999999999999999999 899999999965 999999999999999998888999999999999999998


Q ss_pred             chHHHh
Q psy6490         327 PKEAVQ  332 (398)
Q Consensus       327 ~k~~~~  332 (398)
                      .++...
T Consensus        92 ~~~~~~   97 (109)
T 2dnn_A           92 ERQWVA   97 (109)
T ss_dssp             HHHHHH
T ss_pred             ccchhh
Confidence            776543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=9.4e-19  Score=135.68  Aligned_cols=89  Identities=27%  Similarity=0.430  Sum_probs=82.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      ..+..+.++|||+|||.++++++|+++|++||.|.+|++++++.++.++|||||+|.+.++|++|++ +++..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            3445578999999999999999999999999999999999999999999999999999999999999 999999999999


Q ss_pred             CCCCCCCCCC
Q psy6490         234 PKHATPKNRP  243 (398)
Q Consensus       234 v~~~~~~~~~  243 (398)
                      |.++..+...
T Consensus        89 v~~a~~~~~~   98 (103)
T 2cq0_A           89 VEWAKPSTNS   98 (103)
T ss_dssp             EEESSCCCCS
T ss_pred             EEECCCCCCC
Confidence            9998876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=8.1e-19  Score=138.47  Aligned_cols=87  Identities=17%  Similarity=0.323  Sum_probs=78.6

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE--------ETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI  315 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~--------~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i  315 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.        .|+|++++.+++++|||||+|.+.++|++|+ .||+..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999999        6999999899999999999999988887776 5999999


Q ss_pred             CCEEEEEEecCchHHH
Q psy6490         316 KNKKVECKKAQPKEAV  331 (398)
Q Consensus       316 ~g~~i~v~~a~~k~~~  331 (398)
                      +|+.|+|.|++++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999887543

>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=99.77  E-value=6.7e-20  Score=149.12  Aligned_cols=125  Identities=10%  Similarity=0.072  Sum_probs=75.0

Q ss_pred             cEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCCCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEee
Q psy6490         204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM  283 (398)
Q Consensus       204 g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~  283 (398)
                      |+||.+|..++.+..++........|....-... ...........++|||+|||+++|++||+++|+.|| |++|+|++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g-~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~   79 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSG-DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI   79 (139)
T ss_dssp             --------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCC
T ss_pred             CcccccccCccccchhcccchhccCCCCCCCCCC-CcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEE
Confidence            5788888888777666542222233332211111 111123344567899999999999999999999999 77999999


Q ss_pred             cCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCchHHH
Q psy6490         284 DQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAV  331 (398)
Q Consensus       284 ~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k~~~  331 (398)
                      |+. ++++|||||+|++.++|++|+++|+..|+||.|+|.++..++..
T Consensus        80 d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~~~  126 (139)
T 2hgn_A           80 GPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGAS  126 (139)
T ss_dssp             SSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSCC-
T ss_pred             CCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCCCC
Confidence            975 99999999999999888888899999999999999999877643

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1e-18  Score=134.39  Aligned_cols=83  Identities=12%  Similarity=0.217  Sum_probs=76.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCee-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEE----
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE-ETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKK----  319 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~-~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~----  319 (398)
                      ....++|||+|||.++++++|+++|++||.|. +|+|++|+.+++++|||||+|.+.++|+++++ |||..|+|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34578999999999999999999999999999 99999999999999999999999888877775 9999999999    


Q ss_pred             EEEEecCch
Q psy6490         320 VECKKAQPK  328 (398)
Q Consensus       320 i~v~~a~~k  328 (398)
                      |+|.|+++.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.7e-18  Score=134.71  Aligned_cols=88  Identities=50%  Similarity=0.899  Sum_probs=81.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ......++|||+|||.++++++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++||+.++..|+|+.|.|.
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~   90 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPK   90 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999999888999999999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      ++..+...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99876543

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

Probab=99.77  E-value=6e-19  Score=135.42  Aligned_cols=80  Identities=20%  Similarity=0.320  Sum_probs=70.1

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HC--CceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IH--FHMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~--~~~i~g~~i~v  322 (398)
                      ....++|||+|||+++||++|+++|++||.|++|+|+++      ||||||+|++.++|+++++ ++  +..|+||.|+|
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            346788999999999999999999999999999999876      7999999999888877665 65  57899999999


Q ss_pred             EecCchHHH
Q psy6490         323 KKAQPKEAV  331 (398)
Q Consensus       323 ~~a~~k~~~  331 (398)
                      .|++.+...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876543

>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=99.77  E-value=6e-19  Score=132.60  Aligned_cols=81  Identities=16%  Similarity=0.428  Sum_probs=73.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEec
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR-HRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKA  325 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~-~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~a  325 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+|.++++..++. ++|||||+|.+.++|+++++ |||..|+|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            457899999999999999999999999999999999987766 89999999999888877665 9999999999999999


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.77  E-value=5.6e-19  Score=137.73  Aligned_cols=86  Identities=24%  Similarity=0.454  Sum_probs=77.9

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee---CCEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI---KNKKV  320 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i---~g~~i  320 (398)
                      .....++|||+|||.++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++++ .||+..+   +|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            3456789999999999999999999999999999999999999999999999999988777766 5999998   89999


Q ss_pred             EEEecCchHH
Q psy6490         321 ECKKAQPKEA  330 (398)
Q Consensus       321 ~v~~a~~k~~  330 (398)
                      +|+|+.++..
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999987653

>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=99.77  E-value=9.1e-19  Score=138.69  Aligned_cols=84  Identities=26%  Similarity=0.568  Sum_probs=76.6

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|++||.|++|.|+.+. ++.++|||||+|++.++|++|+ .|||..|+|+.|+|+|+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            456889999999999999999999999999999999997 8999999999999988887766 59999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      +++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

>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=99.77  E-value=1.7e-19  Score=139.08  Aligned_cols=83  Identities=17%  Similarity=0.408  Sum_probs=74.1

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~-~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|+.|| |.+|+|++++ .+|+++|||||+|.+.++|+++++|||..|+|+.|+|++
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEe
Confidence            45678999999999999999999999999 9999999998 689999999999999888877779999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      ++++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98753

>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=99.77  E-value=2.9e-19  Score=141.51  Aligned_cols=102  Identities=11%  Similarity=0.304  Sum_probs=91.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++++++|+++|+.||.|.+|+++++   +.++|||||+|.+.++|.+|++ +++..++|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            6789999999999999999999999999999999875   4469999999999999999999 89999999999999987


Q ss_pred             CCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCC
Q psy6490         239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK  275 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~  275 (398)
                      .....           ++++...++++|+++|++||.
T Consensus        84 ~~~~~-----------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRAF-----------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHT-----------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChhh-----------hhhhHhHhHHHHHHHHHHhCC
Confidence            54331           577888899999999999985

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

Probab=99.77  E-value=2.2e-18  Score=133.62  Aligned_cols=87  Identities=17%  Similarity=0.330  Sum_probs=80.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ......++|||+|||.++++++|+++|+.|| |.+|++++++.+++++|||||+|.+.++|++|+++++..|+|+.|.|.
T Consensus        10 ~~~~~~~~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           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD   88 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEE
Confidence            3344789999999999999999999999997 999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      ++..+...
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            98876543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2e-18  Score=136.93  Aligned_cols=86  Identities=31%  Similarity=0.607  Sum_probs=77.2

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVEC  322 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v  322 (398)
                      ......++|||+|||.++|+++|+++|++||.|++|+|++++.+++++|||||+|.+.++|+++++ +++ .|+|+.|+|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            344567899999999999999999999999999999999999999999999999999888877775 676 899999999


Q ss_pred             EecCchHH
Q psy6490         323 KKAQPKEA  330 (398)
Q Consensus       323 ~~a~~k~~  330 (398)
                      +|+..+..
T Consensus        91 ~~a~~~~~   98 (116)
T 2cqd_A           91 NLAYLGAK   98 (116)
T ss_dssp             EESTTTCC
T ss_pred             EEcccCCC
Confidence            99976543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.2e-18  Score=130.39  Aligned_cols=82  Identities=16%  Similarity=0.305  Sum_probs=75.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||+++++++|+++|+.| .|.+|+|+++ .+|+++|||||+|++.++|+++++||+..|+|+.|+|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEEC
Confidence            3456889999999999999999999999 9999999999 7899999999999998888877779999999999999999


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            8763

>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=99.77  E-value=1.5e-18  Score=137.44  Aligned_cols=88  Identities=23%  Similarity=0.408  Sum_probs=81.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|
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            334477999999999999999999999999999999999999999999999999999999999996 8999999999999


Q ss_pred             CCCCCCCCC
Q psy6490         235 KHATPKNRP  243 (398)
Q Consensus       235 ~~~~~~~~~  243 (398)
                      .++..+...
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpz_A          100 QLKRSKNDS  108 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EEcCCCCcC
Confidence            999876553

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.77  E-value=2.5e-18  Score=134.24  Aligned_cols=81  Identities=15%  Similarity=0.231  Sum_probs=74.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|.|+++. +++++|||||+|.+.++|++|+ .||+..|+|+.|+|+
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            34567899999999999999999999999999999999997 9999999999999988777766 599999999999999


Q ss_pred             ecC
Q psy6490         324 KAQ  326 (398)
Q Consensus       324 ~a~  326 (398)
                      |+.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>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=99.77  E-value=2.5e-18  Score=133.25  Aligned_cols=86  Identities=24%  Similarity=0.516  Sum_probs=75.8

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ......++|||+|||.++++++|+++|++||.|++|+|+++..  .++|||||+|.+.++|++|+ .||+..|+|+.|+|
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 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3445678999999999999999999999999999999998854  38999999999988777766 59999999999999


Q ss_pred             EecCchHHH
Q psy6490         323 KKAQPKEAV  331 (398)
Q Consensus       323 ~~a~~k~~~  331 (398)
                      .|+.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999887543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.4e-18  Score=132.66  Aligned_cols=84  Identities=31%  Similarity=0.484  Sum_probs=78.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|
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            444578999999999999999999999999999999999999999999999999999999999998 8999999999999


Q ss_pred             CCCCC
Q psy6490         235 KHATP  239 (398)
Q Consensus       235 ~~~~~  239 (398)
                      .++..
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            88764

>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=99.77  E-value=2.4e-18  Score=135.24  Aligned_cols=88  Identities=26%  Similarity=0.449  Sum_probs=81.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CC------CcccC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VP------IHTLD  228 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~------~~~~~  228 (398)
                      ......++|||+|||.++++++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++|++ ++      +..++
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            344578999999999999999999999999999999999999999999999999999999999998 77      89999


Q ss_pred             CcccCCCCCCCCCCC
Q psy6490         229 GKKIDPKHATPKNRP  243 (398)
Q Consensus       229 g~~l~v~~~~~~~~~  243 (398)
                      |+.|.|.++..+...
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999876553

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.77  E-value=3e-19  Score=129.98  Aligned_cols=75  Identities=47%  Similarity=0.780  Sum_probs=72.0

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      +|||+|||.++++++|+++|++||.|.+|.+.+++.++.++|||||+|.+.++|++++++++..|+|+.|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999988999999999999985

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.7e-18  Score=134.24  Aligned_cols=87  Identities=30%  Similarity=0.478  Sum_probs=80.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .+..+.++|||+|||.++++++|+++|+.||.|.+|+++.++.+++++|||||+|.+.++|++|++ +++..++|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            344478999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++.....
T Consensus        88 ~~a~~~~~   95 (103)
T 2dnm_A           88 QVARYGRR   95 (103)
T ss_dssp             EECSSCCS
T ss_pred             EECCcCCC
Confidence            99886554

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=5e-18  Score=136.23  Aligned_cols=84  Identities=14%  Similarity=0.213  Sum_probs=76.4

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~  323 (398)
                      .....++|||+||+.++++++|+++|++||.|++|+|+++. +++++|||||+|++.++|+++++ |||..|+|+.|+|+
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            34567899999999999999999999999999999999997 89999999999999888777664 99999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |+.++.
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            997653

>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=99.77  E-value=1.8e-18  Score=132.99  Aligned_cols=85  Identities=29%  Similarity=0.529  Sum_probs=80.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            477999999999999999999999999999999999999899999999999999999999995 9999999999999999


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            877654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=2.4e-18  Score=134.28  Aligned_cols=89  Identities=25%  Similarity=0.457  Sum_probs=81.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeC-CCCCCcccEEEEEEcChHhHHHHHh-C-CCcccCCcc
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKD-PITQRSRGFGFITFAEPETVEKVLK-V-PIHTLDGKK  231 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~-~~~~~~~g~afV~f~~~e~a~~al~-~-~~~~~~g~~  231 (398)
                      .......++|||+|||.++++++|+++|+.||.|.+|+++++ +.++.++|||||+|.+.++|++|++ + ++..|+|+.
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            344557899999999999999999999999999999999999 7899999999999999999999998 7 899999999


Q ss_pred             cCCCCCCCCCCC
Q psy6490         232 IDPKHATPKNRP  243 (398)
Q Consensus       232 l~v~~~~~~~~~  243 (398)
                      |.|.++..+...
T Consensus        89 l~v~~a~~~~~~  100 (107)
T 2cph_A           89 LVLEWADSEVTV  100 (107)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999876553

>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=99.76  E-value=3.5e-19  Score=137.57  Aligned_cols=82  Identities=12%  Similarity=0.147  Sum_probs=74.6

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||+++|++||+++|+.||.| +|+|++|+ +++++|||||+|++.++|++|+++|+..|+||.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            3456789999999999999999999999954 89999997 899999999999999888888899999999999999998


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      ...+
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.76  E-value=2.7e-19  Score=143.63  Aligned_cols=88  Identities=17%  Similarity=0.299  Sum_probs=79.7

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||+++|+++|+++|+.||.|.++.++.+..+++++|||||+|++.++|++|++||+..|+|+.|+|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            34568999999999999999999999999999877778878999999999999999888888889999999999999999


Q ss_pred             CchHHHhh
Q psy6490         326 QPKEAVQA  333 (398)
Q Consensus       326 ~~k~~~~~  333 (398)
                      ..++....
T Consensus       102 ~~~~~~~~  109 (124)
T 1wel_A          102 TKKGMLEK  109 (124)
T ss_dssp             CHHHHHHH
T ss_pred             CHHHHHHH
Confidence            98876543

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

Probab=99.76  E-value=6.3e-19  Score=136.92  Aligned_cols=85  Identities=24%  Similarity=0.397  Sum_probs=77.3

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhh-cCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCce-eCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHM-IKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~-~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~-i~g~~i~v  322 (398)
                      ....++|||+|||.++|+++|+++|+. ||.|.+|.|++|. ++.++|||||+|.+.++|++++ .||+.. |+|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            456789999999999999999999999 9999999999997 9999999999999988777766 599999 99999999


Q ss_pred             EecCchHHH
Q psy6490         323 KKAQPKEAV  331 (398)
Q Consensus       323 ~~a~~k~~~  331 (398)
                      .|+.++..+
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999877644

>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=99.76  E-value=4.6e-19  Score=171.90  Aligned_cols=85  Identities=20%  Similarity=0.436  Sum_probs=78.1

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+||++.+|+++|+++|+.||.|+.|.|+.+..++.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999999999999999999999999988887766 7899999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +.++..
T Consensus       179 a~~~~~  184 (437)
T 3pgw_S          179 ERGRTV  184 (437)
T ss_pred             eCCCCC
Confidence            987654

>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=99.76  E-value=1.3e-18  Score=133.56  Aligned_cols=83  Identities=17%  Similarity=0.202  Sum_probs=75.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|++++ +||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            345688999999999999999999999999999999999899999999999999988776666 7999999999999999


Q ss_pred             cCch
Q psy6490         325 AQPK  328 (398)
Q Consensus       325 a~~k  328 (398)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8754

>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=99.76  E-value=1.9e-18  Score=139.34  Aligned_cols=86  Identities=31%  Similarity=0.487  Sum_probs=80.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ....+.++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..|+|++|.|
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            344578999999999999999999999999999999999999999999999999999999999998 8999999999999


Q ss_pred             CCCCCCC
Q psy6490         235 KHATPKN  241 (398)
Q Consensus       235 ~~~~~~~  241 (398)
                      .++..+.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9987654

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

Probab=99.76  E-value=2.6e-18  Score=132.43  Aligned_cols=85  Identities=16%  Similarity=0.356  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|+++.++ +++++|||||+|.+.++|++|++ +++..++|+.|.|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34478999999999999999999999999999999999998 89999999999999999999996 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++.++..
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9876543

>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=99.76  E-value=2.2e-18  Score=133.82  Aligned_cols=86  Identities=21%  Similarity=0.480  Sum_probs=79.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCC-CCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT-QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~-~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.|| |.+|+|++++.+ ++++|||||+|.+.++|++||.+++..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVD   89 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEE
Confidence            344779999999999999999999999999 999999999987 999999999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      ++..+...
T Consensus        90 ~a~~~~~~   97 (104)
T 1wi8_A           90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            98876553

>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=99.76  E-value=1.2e-18  Score=135.21  Aligned_cols=84  Identities=23%  Similarity=0.317  Sum_probs=76.4

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE-TVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~-v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||+++|+++|+++|+.||.|.+ |+|+++ .+++++|||||+|++.++|++|++.|+..|+||.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEE
Confidence            345689999999999999999999999999998 888888 789999999999999999988887799999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +..++.
T Consensus        91 ~~~~~~   96 (104)
T 1wg5_A           91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHH
Confidence            876653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.2e-18  Score=134.57  Aligned_cols=83  Identities=22%  Similarity=0.302  Sum_probs=75.0

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|++||.|++|+|++++ +++++|||||+|++.++|++++ .||+..|+|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            4457899999999999999999999999999999999996 6999999999999988777766 5999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      ++...
T Consensus        91 a~~~~   95 (114)
T 2do0_A           91 DERAL   95 (114)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            87643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=7.3e-19  Score=139.98  Aligned_cols=85  Identities=24%  Similarity=0.321  Sum_probs=77.7

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCe----eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKV----EETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECK  323 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i----~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~  323 (398)
                      ...+|||+|||+++|++||+++|+.||.|    .+|+|++| .+|+++|||||+|++.++|++|+++|+..|+||.|+|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            46789999999999999999999999975    68999998 58999999999999999999988889999999999999


Q ss_pred             ecCchHHHhh
Q psy6490         324 KAQPKEAVQA  333 (398)
Q Consensus       324 ~a~~k~~~~~  333 (398)
                      .+..++....
T Consensus       101 ~a~~~e~~~~  110 (123)
T 2dha_A          101 RSTAAEVQQV  110 (123)
T ss_dssp             EECHHHHHHH
T ss_pred             ECCHHHHHHH
Confidence            9988876654

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

Probab=99.76  E-value=2e-18  Score=131.15  Aligned_cols=79  Identities=10%  Similarity=0.136  Sum_probs=68.6

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCce--eCCEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHM--IKNKKVE  321 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~--i~g~~i~  321 (398)
                      ...++++|||+|||+++|+++|+++|++||.|++|+++++      ||||||+|++.++|++|+ .|++..  |+||.|+
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 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            3456789999999999999999999999999999998754      789999999988776665 577764  8999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |.|++.++
T Consensus        91 V~~S~~k~   98 (100)
T 3r27_A           91 VNYSTSQK   98 (100)
T ss_dssp             EEECSCSC
T ss_pred             EEeccccc
Confidence            99998763

>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=99.76  E-value=9.9e-19  Score=133.43  Aligned_cols=80  Identities=18%  Similarity=0.241  Sum_probs=73.0

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||+++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|++++ .||+..|+|+.|+|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            4588999999999999999999999999999999999999999999999999988777666 599999999999999986


Q ss_pred             c
Q psy6490         327 P  327 (398)
Q Consensus       327 ~  327 (398)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.76  E-value=2.7e-19  Score=135.93  Aligned_cols=81  Identities=20%  Similarity=0.400  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCC--EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCc----ccCCcc
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIH----TLDGKK  231 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~--i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~----~~~g~~  231 (398)
                      ..-.+|||+|||+++|+++|+++|++||.  |.+|++++|+.+|++||||||+|.+.++|++|++ +++.    .++||+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            36789999999999999999999999995  6799999999999999999999999999999998 6654    589999


Q ss_pred             cCCCCCCC
Q psy6490         232 IDPKHATP  239 (398)
Q Consensus       232 l~v~~~~~  239 (398)
                      |.|++++.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99998764

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

Probab=99.76  E-value=2.1e-18  Score=137.14  Aligned_cols=82  Identities=23%  Similarity=0.403  Sum_probs=77.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .+..+.++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..++|++|.|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344578999999999999999999999999999999999999899999999999999999999998 8999999999998


Q ss_pred             CCC
Q psy6490         235 KHA  237 (398)
Q Consensus       235 ~~~  237 (398)
                      +++
T Consensus       115 ~~a  117 (118)
T 2khc_A          115 QLK  117 (118)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            875

>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=99.76  E-value=4.2e-18  Score=130.17  Aligned_cols=80  Identities=19%  Similarity=0.170  Sum_probs=71.9

Q ss_pred             ccccceeecCCCCCCCHHHHH----HHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~----~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      ...++|||+|||+++++++|+    ++|++||.|++|+|++|+.+   +|||||+|++.++|++|+ .|||..|+|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            356789999999999999999    99999999999999998655   899999999988776666 5999999999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |+|++++.
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997654

>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=99.76  E-value=4.6e-18  Score=131.76  Aligned_cols=87  Identities=39%  Similarity=0.615  Sum_probs=79.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ....+.++|||+|||.++++++|+++|+.||.|.+|+++.++.+++++|||||+|.+.++|++|++ ++..++|+.|.|.
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~   88 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEE
Confidence            344578999999999999999999999999999999999999999999999999999999999999 4678999999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      ++..+...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99876653

>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=99.76  E-value=1.9e-18  Score=128.30  Aligned_cols=81  Identities=27%  Similarity=0.459  Sum_probs=76.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      +.+|||+|||.++++++|+++|+.||.|.++++++++.++.++|||||+|.+.++|++|++ +++..++|+.|.|.++..
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            4689999999999999999999999999999999999899999999999999999999998 899999999999999876


Q ss_pred             CC
Q psy6490         240 KN  241 (398)
Q Consensus       240 ~~  241 (398)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.76  E-value=5.3e-19  Score=138.03  Aligned_cols=87  Identities=18%  Similarity=0.243  Sum_probs=79.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGK---VEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~---i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v  322 (398)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++++++|+..|+||.|+|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEE
Confidence            456788999999999999999999999998   89999999976 99999999999999999888889999999999999


Q ss_pred             EecCchHHHhh
Q psy6490         323 KKAQPKEAVQA  333 (398)
Q Consensus       323 ~~a~~k~~~~~  333 (398)
                      .++.+++....
T Consensus        87 ~~a~~~~~~~~   97 (107)
T 2lmi_A           87 YEINNEDVDAL   97 (107)
T ss_dssp             EECCHHHHHHH
T ss_pred             EECCHHHHHHH
Confidence            99998776544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.76  E-value=2.8e-18  Score=125.62  Aligned_cols=73  Identities=7%  Similarity=0.192  Sum_probs=65.5

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      +..|||+||++.+||++|+++|.+||+|.++.+..      +||||||+|.++++| +|+..||+..++||.|+|++|..
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            56799999999999999999999999999999865      599999999997555 55567999999999999999953

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=131.42  Aligned_cols=82  Identities=27%  Similarity=0.493  Sum_probs=76.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34478999999999999999999999999999999999999999999999999999999999997 99999999999988


Q ss_pred             CCC
Q psy6490         236 HAT  238 (398)
Q Consensus       236 ~~~  238 (398)
                      +++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            763

>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=99.76  E-value=6.3e-19  Score=133.09  Aligned_cols=81  Identities=20%  Similarity=0.461  Sum_probs=71.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC--CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFG--AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G--~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+|||+|||.++|+++|+++|+.||  .|.+++++.|+.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.++.
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            5899999999999999999999999  99999999999999999999999999999999997 99999999999999987


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

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

Probab=99.76  E-value=1.8e-18  Score=133.60  Aligned_cols=80  Identities=14%  Similarity=0.280  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +...++|||+|||.++|+++|+++|+.||.|.+|++++++. |.++|||||+|.+.++|.+|+++++..++|+.|.|.+.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34679999999999999999999999999999999999987 99999999999999999999999999999999998765


Q ss_pred             C
Q psy6490         238 T  238 (398)
Q Consensus       238 ~  238 (398)
                      .
T Consensus        87 ~   87 (103)
T 1s79_A           87 D   87 (103)
T ss_dssp             H
T ss_pred             h
Confidence            4

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=132.26  Aligned_cols=87  Identities=28%  Similarity=0.424  Sum_probs=79.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .....+.++|||+|||.++|+++|+++|+.||.|.+|+++.+  ++.++|||||+|.+.++|++|++ +++..++|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            344558899999999999999999999999999999999998  88999999999999999999998 899999999999


Q ss_pred             CCCCCCCCCC
Q psy6490         234 PKHATPKNRP  243 (398)
Q Consensus       234 v~~~~~~~~~  243 (398)
                      |.++..+...
T Consensus        87 V~~a~~~~~~   96 (103)
T 2d9p_A           87 VALAQRKEER   96 (103)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEecccccC
Confidence            9999876553

>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=99.76  E-value=4.1e-18  Score=142.46  Aligned_cols=86  Identities=19%  Similarity=0.304  Sum_probs=78.4

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++|+++|+++|++||.|++|.|++++.++.++|||||+|++.++|++|++ ||+..|+|+.|+|+|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3467899999999999999999999999999999999999999999999999999888877665 899999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      ++++...
T Consensus       116 a~~~~~~  122 (156)
T 1h2v_Z          116 DAGFKEG  122 (156)
T ss_dssp             ESCCCTT
T ss_pred             CCCCCCc
Confidence            9875543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=4.2e-18  Score=129.89  Aligned_cols=84  Identities=33%  Similarity=0.622  Sum_probs=79.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            67999999999999999999999999999999999999999999999999999999999998 89999999999999988


Q ss_pred             CCCCC
Q psy6490         239 PKNRP  243 (398)
Q Consensus       239 ~~~~~  243 (398)
                      .+...
T Consensus        84 ~~~~~   88 (95)
T 2dnz_A           84 ERLDG   88 (95)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            76553

>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=99.75  E-value=1.3e-18  Score=130.49  Aligned_cols=81  Identities=30%  Similarity=0.518  Sum_probs=75.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +.++|||+|||.++++++|+++|+.||.|.++++++++.++.++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            67899999999999999999999999999999999999899999999999999999999998 89999999999998876


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      .+
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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=99.75  E-value=1.2e-18  Score=140.24  Aligned_cols=88  Identities=14%  Similarity=0.300  Sum_probs=79.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++|+++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|++|+ .||+..|+|+.|+|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3445789999999999999999999999999999999999889999999999999988887776 699999999999999


Q ss_pred             ecCchHHHh
Q psy6490         324 KAQPKEAVQ  332 (398)
Q Consensus       324 ~a~~k~~~~  332 (398)
                      |+.++....
T Consensus        98 ~a~~~~~~~  106 (126)
T 3ex7_B           98 WCFVRGPPK  106 (126)
T ss_dssp             ESEESSSCC
T ss_pred             EecCCCCCC
Confidence            998765443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.9e-18  Score=133.70  Aligned_cols=85  Identities=35%  Similarity=0.679  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3478999999999999999999999999999999999999999999999999999999999996 899999999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +..+..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            876654

>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=99.75  E-value=5.5e-18  Score=132.38  Aligned_cols=85  Identities=32%  Similarity=0.613  Sum_probs=79.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34477999999999999999999999999999999999999899999999999999999999998 89999999999999


Q ss_pred             CCCCCC
Q psy6490         236 HATPKN  241 (398)
Q Consensus       236 ~~~~~~  241 (398)
                      ++..+.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            987653

>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=99.75  E-value=2e-18  Score=135.33  Aligned_cols=86  Identities=17%  Similarity=0.364  Sum_probs=76.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCC-eeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHH-HC--CceeCCEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGK-VEETVML-MDQQTKRHRGFGFVTFENEEVVDHICE-IH--FHMIKNKKVE  321 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~-i~~v~i~-~~~~~~~~kg~afV~F~~~eaa~a~~~-l~--~~~i~g~~i~  321 (398)
                      ...++|||+|||.++|+++|+++|++||. |.+|.++ .+..++.++|||||+|.+.++|+++++ |+  +..|+|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35688999999999999999999999998 9999998 788889999999999999888877764 75  5899999999


Q ss_pred             EEecCchHHHh
Q psy6490         322 CKKAQPKEAVQ  332 (398)
Q Consensus       322 v~~a~~k~~~~  332 (398)
                      |.|+.++....
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99999876543

>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=99.75  E-value=3.1e-18  Score=131.50  Aligned_cols=82  Identities=20%  Similarity=0.269  Sum_probs=70.6

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-H--CCceeCCEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I--HFHMIKNKKV  320 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l--~~~~i~g~~i  320 (398)
                      ......++|||+|||+++++++|+++|++||.|++|+++++      ||||||+|++.++|++|++ |  ++..|+|+.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            34456789999999999999999999999999999998765      8999999999887766664 4  6788999999


Q ss_pred             EEEecCchHHH
Q psy6490         321 ECKKAQPKEAV  331 (398)
Q Consensus       321 ~v~~a~~k~~~  331 (398)
                      +|.|++.+...
T Consensus        84 ~V~~a~~~~~~   94 (101)
T 2cq1_A           84 YIQYSNHKELK   94 (101)
T ss_dssp             EEEECSCSSCC
T ss_pred             EEEEcCcccCc
Confidence            99999876543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.75  E-value=1.9e-18  Score=135.32  Aligned_cols=87  Identities=54%  Similarity=0.973  Sum_probs=76.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      ....+.++|||+|||.++++++|+++|+.||.|.+|++++++.+|.++|||||+|.+.++|++|++.++..++|+.|.|.
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~   99 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   99 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999999976789999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++..+..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9876654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-18  Score=134.70  Aligned_cols=86  Identities=30%  Similarity=0.446  Sum_probs=80.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            3478999999999999999999999999999999999999899999999999999999999997 899999999999999


Q ss_pred             CCCCCCC
Q psy6490         237 ATPKNRP  243 (398)
Q Consensus       237 ~~~~~~~  243 (398)
                      +..+...
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8876554

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=1.7e-18  Score=140.39  Aligned_cols=87  Identities=22%  Similarity=0.411  Sum_probs=79.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEE--EEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCc----ccC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD--VLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIH----TLD  228 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~--~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~----~~~  228 (398)
                      ..+...++|||+|||+++|+++|+++|++||.|..  |+|++|+.+|++||||||+|.+. +|.+|++ +++.    .++
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            33457899999999999999999999999999976  99999999999999999999999 9999998 8898    999


Q ss_pred             CcccCCCCCCCCCCC
Q psy6490         229 GKKIDPKHATPKNRP  243 (398)
Q Consensus       229 g~~l~v~~~~~~~~~  243 (398)
                      |+.|.|+++..+...
T Consensus        97 gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           97 GKTINVEFAKGSKRD  111 (131)
T ss_dssp             GCCCCCEECCCSCCC
T ss_pred             CEEEEEEECCCCCCC
Confidence            999999999876543

>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=99.75  E-value=7.4e-18  Score=131.05  Aligned_cols=85  Identities=22%  Similarity=0.377  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC---cccC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG---KKID  233 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g---~~l~  233 (398)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|++++ +++++|||||+|.+.++|++|++ +++..+.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3468999999999999999999999999999999999998 79999999999999999999998 89999888   9999


Q ss_pred             CCCCCCCCCC
Q psy6490         234 PKHATPKNRP  243 (398)
Q Consensus       234 v~~~~~~~~~  243 (398)
                      |.++..+...
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9998876543

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

Probab=99.75  E-value=3.1e-18  Score=134.13  Aligned_cols=84  Identities=25%  Similarity=0.546  Sum_probs=74.4

Q ss_pred             CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       243 ~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      .......++|||+|||.++++++|+++|++||.|++|+++++.  +.++|||||+|++.++|++++ .|||..|+|+.|+
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3445567899999999999999999999999999999999985  348999999999987776666 5999999999999


Q ss_pred             EEecCch
Q psy6490         322 CKKAQPK  328 (398)
Q Consensus       322 v~~a~~k  328 (398)
                      |+|++++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999876

>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=99.75  E-value=3.4e-19  Score=134.57  Aligned_cols=81  Identities=33%  Similarity=0.648  Sum_probs=70.7

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCchH
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      ++|||+|||.++++++|+++|++||.|++|.+.+++.+++++|||||+|++.++.+++..|||..|+|+.|+|+++.++.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTHHHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            57999999999999999999999999999999999999999999999999977445555699999999999999998765


Q ss_pred             H
Q psy6490         330 A  330 (398)
Q Consensus       330 ~  330 (398)
                      .
T Consensus        82 ~   82 (90)
T 2ki2_A           82 S   82 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.75  E-value=3.1e-18  Score=133.47  Aligned_cols=88  Identities=25%  Similarity=0.430  Sum_probs=80.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc---CCcc
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL---DGKK  231 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~---~g~~  231 (398)
                      ..+...++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..+   .|+.
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            344578999999999999999999999999999999999999999999999999999999999998 888887   8999


Q ss_pred             cCCCCCCCCCCC
Q psy6490         232 IDPKHATPKNRP  243 (398)
Q Consensus       232 l~v~~~~~~~~~  243 (398)
                      |.|.++..+...
T Consensus        88 l~v~~a~~~~~~   99 (106)
T 2dgp_A           88 IQVKPADSESRG   99 (106)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEECCccccc
Confidence            999998876553

>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=99.75  E-value=3.9e-18  Score=133.81  Aligned_cols=94  Identities=17%  Similarity=0.391  Sum_probs=81.6

Q ss_pred             cCCcccCCCCCCCCCCCccCccccceeecCCCCC-CCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHH
Q psy6490         227 LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD  305 (398)
Q Consensus       227 ~~g~~l~v~~~~~~~~~~~~~~~~~l~V~nLp~~-~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~  305 (398)
                      ..|..|.+..+............++|||+|||.+ +++++|+++|++||.|++|.|        ++|||||+|++.++|+
T Consensus         5 ~~g~~~~~~~s~~~~~~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~   76 (110)
T 1wf1_A            5 SSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHAR   76 (110)
T ss_dssp             CCSCCCCCCCCCSCCSCCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHH
T ss_pred             CCCcccccccCCCCCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHH
Confidence            4677888888776666666666789999999999 999999999999999999988        4789999999977776


Q ss_pred             HHH-HHCCceeCCEEEEEEecCch
Q psy6490         306 HIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       306 a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      +++ +||+..|+|+.|+|.|++..
T Consensus        77 ~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           77 AAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             HHHHHHTTCEETTEECCEEESCCC
T ss_pred             HHHHHcCCCEECCeEEEEEECCCC
Confidence            666 79999999999999999754

>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=99.75  E-value=5.8e-18  Score=131.40  Aligned_cols=83  Identities=23%  Similarity=0.351  Sum_probs=76.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEE-EEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD-VLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~-~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+|||+++|+++|+++|+.||.|.+ |+|+.+ .+|+++|||||+|.+.++|++||+.++..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEE
Confidence            346799999999999999999999999999987 888888 689999999999999999999999999999999999988


Q ss_pred             CCCCC
Q psy6490         237 ATPKN  241 (398)
Q Consensus       237 ~~~~~  241 (398)
                      +....
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            76544

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

Probab=99.75  E-value=1.3e-17  Score=129.52  Aligned_cols=84  Identities=25%  Similarity=0.384  Sum_probs=78.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhc-CCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcc-cCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGM-FGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHT-LDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~-~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~-~~g~~l~v  234 (398)
                      ....++|||+|||.++|+++|+++|+. ||.|.+|++++++ +++++|||||+|.+.++|++|++ +++.. ++|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            347799999999999999999999999 9999999999999 99999999999999999999999 89999 99999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++..+..
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99976654

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

Probab=99.75  E-value=4.4e-18  Score=128.99  Aligned_cols=82  Identities=21%  Similarity=0.385  Sum_probs=74.0

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|++||.|++|+|.++  +++++|||||+|.+.++|++++ .||+..|+|+.|+|+|
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            345789999999999999999999999999999999885  7899999999999988777666 5999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      ++++.
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98764

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

Probab=99.75  E-value=1.2e-18  Score=127.51  Aligned_cols=76  Identities=42%  Similarity=0.719  Sum_probs=69.9

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ++|||+|||.++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|+++++..+..|+|+.|+|+||
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            4799999999999999999999999999999999988999999999999998888777764339999999999997

>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=99.75  E-value=2.4e-18  Score=131.50  Aligned_cols=83  Identities=20%  Similarity=0.416  Sum_probs=78.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ++++|||+|||.++++++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.++.
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            36899999999999999999999999999999999999999999999999999999999997 89999999999999988


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      .+..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7654

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

Probab=99.75  E-value=1.3e-18  Score=134.28  Aligned_cols=92  Identities=22%  Similarity=0.449  Sum_probs=81.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      ++|||+|||.++|+++|+++|++||.|.+|++.++     ++|||||+|.+.++|++|++ +++..++|+.|.|.++..+
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            48999999999999999999999999999999987     68999999999999999998 8999999999999988775


Q ss_pred             CCCcc-------CccccceeecCCC
Q psy6490         241 NRPKI-------GNRTKKIFVGGVS  258 (398)
Q Consensus       241 ~~~~~-------~~~~~~l~V~nLp  258 (398)
                      .....       .....+|||+||+
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCC
Confidence            53322       2236789999996

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.75  E-value=4.7e-18  Score=130.70  Aligned_cols=81  Identities=20%  Similarity=0.404  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEE--------EEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD--------VLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~--------~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      .....++|||+|||.++++++|+++|++||.|.+        +++++++.+|+++|||||+|.+.++|++|++ +++..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3447899999999999999999999999999999        9999999999999999999999999999998 899999


Q ss_pred             CCcccCCCCC
Q psy6490         228 DGKKIDPKHA  237 (398)
Q Consensus       228 ~g~~l~v~~~  237 (398)
                      +|+.|.|.++
T Consensus        89 ~g~~l~V~~A   98 (99)
T 2la6_A           89 SGNPIKVSFA   98 (99)
T ss_dssp             SSSBCEEEEC
T ss_pred             CCcEEEEEec
Confidence            9999998875

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

Probab=99.75  E-value=4.7e-18  Score=130.43  Aligned_cols=81  Identities=19%  Similarity=0.263  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CC--CcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VP--IHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~--~~~~~g~~l~v  234 (398)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+++      ||||||+|.+.++|++|++ ++  +..++|+.|.|
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            347899999999999999999999999999999999875      7999999999999999998 54  46899999999


Q ss_pred             CCCCCCCCCc
Q psy6490         235 KHATPKNRPK  244 (398)
Q Consensus       235 ~~~~~~~~~~  244 (398)
                      .++..+....
T Consensus        87 ~~A~~~~~~~   96 (105)
T 1sjq_A           87 QFSNHKELKT   96 (105)
T ss_dssp             CCCSSSSCCC
T ss_pred             EEcCCCCCCc
Confidence            9998765543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=5.1e-18  Score=130.49  Aligned_cols=83  Identities=25%  Similarity=0.379  Sum_probs=78.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEE-EEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcc----c
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVT-DVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKK----I  232 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~-~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~----l  232 (398)
                      ...++|||+|||.++++++|+++|++||.|. +|++++++.+++++|||||+|.+.++|++|++ +++..++|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3789999999999999999999999999999 99999999999999999999999999999999 8999999999    9


Q ss_pred             CCCCCCCCC
Q psy6490         233 DPKHATPKN  241 (398)
Q Consensus       233 ~v~~~~~~~  241 (398)
                      .|.++....
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            998887654

>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=99.75  E-value=2.2e-18  Score=128.63  Aligned_cols=80  Identities=31%  Similarity=0.466  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            378999999999999999999999999999999999998899999999999999999999996 8999999999998876


Q ss_pred             C
Q psy6490         238 T  238 (398)
Q Consensus       238 ~  238 (398)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=5.2e-19  Score=132.03  Aligned_cols=80  Identities=15%  Similarity=0.424  Sum_probs=73.5

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|++++ .|||..|+|+.|+|.|.
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            35688999999999999999999999999999999999999999999999999988777666 59999999999998876


Q ss_pred             C
Q psy6490         326 Q  326 (398)
Q Consensus       326 ~  326 (398)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.74  E-value=3.5e-18  Score=133.17  Aligned_cols=83  Identities=16%  Similarity=0.316  Sum_probs=78.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|+++.++.+|.++|||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            3467999999999999999999999999999999999999999999999999999999999998 899999999999998


Q ss_pred             CCCC
Q psy6490         237 ATPK  240 (398)
Q Consensus       237 ~~~~  240 (398)
                      +..+
T Consensus       100 a~~~  103 (106)
T 1p27_B          100 CFVR  103 (106)
T ss_dssp             SEES
T ss_pred             ecCC
Confidence            8654

>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=1.1e-18  Score=139.30  Aligned_cols=82  Identities=20%  Similarity=0.330  Sum_probs=74.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCee--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE--ETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~--~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ...++|||+|||+++|+++|+++|+.| .|.  +|+|++|+. |+++|||||+|++.++|++|+++++..|+||.|+|.+
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            456789999999999999999999999 666  899999976 9999999999999999999888899999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +..++.
T Consensus       118 a~~~e~  123 (126)
T 2hgm_A          118 SSQEEV  123 (126)
T ss_dssp             ECHHHH
T ss_pred             CCHHHh
Confidence            987664

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.1e-18  Score=133.86  Aligned_cols=88  Identities=20%  Similarity=0.372  Sum_probs=81.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEE--------EEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcc
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHT  226 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~  226 (398)
                      .+....++|||+|||.++++++|+++|+.||.|.        .|+++.++.+++++|||||+|.+.++|++|++ +++..
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            3455789999999999999999999999999999        69999998899999999999999999999998 89999


Q ss_pred             cCCcccCCCCCCCCCCC
Q psy6490         227 LDGKKIDPKHATPKNRP  243 (398)
Q Consensus       227 ~~g~~l~v~~~~~~~~~  243 (398)
                      |+|+.|.|.++..+...
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            99999999998876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.74  E-value=1.7e-18  Score=133.95  Aligned_cols=84  Identities=29%  Similarity=0.539  Sum_probs=76.3

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|++++ +++++|||||+|++.++|+++++ ++..|+|+.|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            3456899999999999999999999999999999999997 99999999999999888888888 999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      .++...
T Consensus        84 ~~~~~~   89 (102)
T 2xs2_A           84 IRKQNL   89 (102)
T ss_dssp             EECC--
T ss_pred             CcCcch
Confidence            877654

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

Probab=99.74  E-value=1.8e-18  Score=125.84  Aligned_cols=75  Identities=45%  Similarity=0.812  Sum_probs=71.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +|||+|||.++++++|+++|++||.|.++++.+++.+++++|||||+|.+.++|++|+++++..++|+.|.|+++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            589999999999999999999999999999999998999999999999999999999999999999999988764

>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=99.74  E-value=3.2e-18  Score=132.16  Aligned_cols=82  Identities=15%  Similarity=0.243  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||+++|+++|+++|+.||. ++|+|++|+ +++++|||||+|.+.++|++||++++..|+|+.|.|..+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            346789999999999999999999999995 599999998 899999999999999999999999999999999999877


Q ss_pred             CCCC
Q psy6490         238 TPKN  241 (398)
Q Consensus       238 ~~~~  241 (398)
                      ....
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>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=99.74  E-value=3.5e-18  Score=151.66  Aligned_cols=84  Identities=11%  Similarity=0.251  Sum_probs=76.4

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEe
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKK  324 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G--~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~  324 (398)
                      ..++|||+||++++|+++|+++|++||  .|++|+|++|+.++++||||||+|++.++|++|++ ||++.|+|+.|+|+|
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  99999999999999999999999999888877775 999999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      ++++...
T Consensus       147 a~~~~~~  153 (229)
T 3q2s_C          147 VNKQFLS  153 (229)
T ss_dssp             CCHHHHH
T ss_pred             CCCCccc
Confidence            9876543

>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=99.74  E-value=6e-18  Score=132.94  Aligned_cols=83  Identities=20%  Similarity=0.303  Sum_probs=73.7

Q ss_pred             ccccceeecCCCCCCCHHHHH---HHHhhcCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHH-HHCCceeCCEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVK---AYFSQFGKVEETVMLMDQQTK---RHRGFGFVTFENEEVVDHIC-EIHFHMIKNKK  319 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~---~~F~~~G~i~~v~i~~~~~~~---~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~  319 (398)
                      ...++|||+|||+++++++|+   ++|++||.|.+|.|+++..++   +++|||||+|++.++|++|+ .||+..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346789999999999999999   999999999999999987654   56699999999988776666 58999999999


Q ss_pred             EEEEecCchH
Q psy6490         320 VECKKAQPKE  329 (398)
Q Consensus       320 i~v~~a~~k~  329 (398)
                      |+|.|+.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998775

>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=99.74  E-value=1.2e-17  Score=130.82  Aligned_cols=81  Identities=16%  Similarity=0.327  Sum_probs=72.4

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++|+++|+++|++||.|++|+|..+   +.++|||||+|++.++|++++ .||+..|+|+.|+|+|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            446789999999999999999999999999999998654   457999999999988887766 7999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      ++++.
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            98764

>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=99.74  E-value=2.7e-18  Score=132.26  Aligned_cols=84  Identities=20%  Similarity=0.487  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCC-CCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.|| |.+|++++++ .+|+++|||||+|.+.++|++|+++++..++|+.|.|.
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVD   93 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEE
Confidence            344789999999999999999999999999 9999999998 68999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy6490         236 HATPKN  241 (398)
Q Consensus       236 ~~~~~~  241 (398)
                      ++..+.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            987653

>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=99.74  E-value=2.2e-18  Score=132.27  Aligned_cols=78  Identities=10%  Similarity=0.140  Sum_probs=67.9

Q ss_pred             CccccceeecCCCC-CCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCC--ceeCCEEEE
Q psy6490         246 GNRTKKIFVGGVSQ-DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHF--HMIKNKKVE  321 (398)
Q Consensus       246 ~~~~~~l~V~nLp~-~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~--~~i~g~~i~  321 (398)
                      ....++|||+|||+ ++|++||+++|++||.|.+|+|+++      +|||||+|++.++|++|+ .||+  ..|+||.|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            44678999999999 9999999999999999999999876      589999999987776665 5664  569999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |.|++.+.
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99998654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=4.8e-18  Score=130.38  Aligned_cols=84  Identities=33%  Similarity=0.595  Sum_probs=78.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCC---CCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI---TQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~---~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      +.++|||+|||.++++++|+++|+.||.|.+|++.+++.   ++.++|||||+|.+.++|++|++ +++..++|+.|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            679999999999999999999999999999999999876   66899999999999999999999 89999999999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      ++..+...
T Consensus        84 ~a~~~~~~   91 (98)
T 2cpf_A           84 ISERATKP   91 (98)
T ss_dssp             CSSCSSCC
T ss_pred             EccCCCCC
Confidence            99876554

>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=99.74  E-value=2e-18  Score=136.42  Aligned_cols=83  Identities=10%  Similarity=0.180  Sum_probs=77.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCE-EEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAV-TDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i-~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||+++|+++|+++|+.||.| .+|+|++|+ +|+++|||||+|.+.++|++||++++..|+|+.|.|
T Consensus        10 ~~~~~~~~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           10 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFV   88 (114)
T ss_dssp             SCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEE
T ss_pred             CCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEE
Confidence            344577999999999999999999999999999 899999998 999999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy6490         235 KHATP  239 (398)
Q Consensus       235 ~~~~~  239 (398)
                      .++..
T Consensus        89 ~~a~~   93 (114)
T 2cpy_A           89 HVVTL   93 (114)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.9e-18  Score=127.23  Aligned_cols=79  Identities=19%  Similarity=0.425  Sum_probs=75.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +.++|||+|||.++++++|+++|++||.|.+++++.++.++.++|||||+|.+.++|++|++ +++..++|+.|++.+..
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            67999999999999999999999999999999999999999999999999999999999998 89999999999988764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=4.8e-19  Score=136.84  Aligned_cols=83  Identities=20%  Similarity=0.403  Sum_probs=75.5

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.. .++++..+++++|||||+|.+.++|+++++||+..|+|+.|+|.++.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcC
Confidence            45679999999999999999999999999988 77778788999999999999988888877899999999999999998


Q ss_pred             chHH
Q psy6490         327 PKEA  330 (398)
Q Consensus       327 ~k~~  330 (398)
                      ++..
T Consensus        94 ~~~~   97 (101)
T 1fj7_A           94 GRDG   97 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.74  E-value=1.5e-17  Score=128.85  Aligned_cols=87  Identities=28%  Similarity=0.541  Sum_probs=78.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .......++|||+|||.++++++|+++|+.||.|.+|++++++.  .++|||||+|.+.++|++|++ +++..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34455789999999999999999999999999999999999863  389999999999999999998 899999999999


Q ss_pred             CCCCCCCCCC
Q psy6490         234 PKHATPKNRP  243 (398)
Q Consensus       234 v~~~~~~~~~  243 (398)
                      |.++..+...
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cq3_A           87 VNNATARVMT   96 (103)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEcccCCCC
Confidence            9998876553

>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=99.74  E-value=1e-17  Score=129.79  Aligned_cols=86  Identities=20%  Similarity=0.346  Sum_probs=77.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .+....++|||+|||.++++++|+++|+.||.|.+|++++++.+  ++|||||+|.+.++|++|++ +++..++|+.|.|
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            44557899999999999999999999999999999999998543  68999999999999999998 8999999999999


Q ss_pred             CCCCCCCCC
Q psy6490         235 KHATPKNRP  243 (398)
Q Consensus       235 ~~~~~~~~~  243 (398)
                      .++......
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            999876543

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.4e-17  Score=131.51  Aligned_cols=82  Identities=21%  Similarity=0.441  Sum_probs=73.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee--------C
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI--------K  316 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i--------~  316 (398)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+++. ++.++|||||+|.+.++|++++ .|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            4456889999999999999999999999999999999997 8999999999999987776666 5999999        5


Q ss_pred             CEEEEEEecCch
Q psy6490         317 NKKVECKKAQPK  328 (398)
Q Consensus       317 g~~i~v~~a~~k  328 (398)
                      ++.|+|+|+.++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999999864

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=4e-18  Score=130.29  Aligned_cols=84  Identities=27%  Similarity=0.449  Sum_probs=79.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEE-EEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDV-LIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~-~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ..++|||+|||.++++++|+++|+.||.|.++ ++++++.++.++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            67999999999999999999999999999999 999998899999999999999999999999 8999999999999998


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            876543

>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=99.74  E-value=8.8e-18  Score=132.98  Aligned_cols=83  Identities=37%  Similarity=0.668  Sum_probs=77.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|++..++ +++++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            367999999999999999999999999999999999998 99999999999999999999998 8999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      .....
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            76543

>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=99.73  E-value=6.7e-18  Score=127.11  Aligned_cols=81  Identities=23%  Similarity=0.481  Sum_probs=77.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      +.++|||+|||.++++++|+++|+.||.|.++++.+++.+++++|||||+|.+.++|++|+.+++..++|+.|.|.++..
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             C
Q psy6490         240 K  240 (398)
Q Consensus       240 ~  240 (398)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.73  E-value=6.2e-18  Score=133.10  Aligned_cols=80  Identities=20%  Similarity=0.320  Sum_probs=70.0

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HC--CceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IH--FHMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~--~~~i~g~~i~v  322 (398)
                      ....++|||+|||+++||++|+++|++||.|++|+|+++      ||||||+|++.++|++|++ ++  +..|+|+.|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345788999999999999999999999999999999876      7999999999888877664 65  56899999999


Q ss_pred             EecCchHHH
Q psy6490         323 KKAQPKEAV  331 (398)
Q Consensus       323 ~~a~~k~~~  331 (398)
                      .|++.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999877544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.73  E-value=1.6e-18  Score=133.47  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCC------CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC-c
Q psy6490         159 PTSAKLFVGGLSW------QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG-K  230 (398)
Q Consensus       159 ~~~~~l~v~nLp~------~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g-~  230 (398)
                      ..+++|||+|||.      ++++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|++|++ +++..++| +
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            3578999999999      99999999999999999999999999999999999999999999999997 89999999 9


Q ss_pred             ccCCCCCCC
Q psy6490         231 KIDPKHATP  239 (398)
Q Consensus       231 ~l~v~~~~~  239 (398)
                      .|.|.++.+
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999988754

>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=99.73  E-value=6.1e-18  Score=129.01  Aligned_cols=82  Identities=29%  Similarity=0.465  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|++.+++. ++++|||||+|.+.++|++|++ +++..++|+.|.|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            344789999999999999999999999999999999999985 8999999999999999999998 89999999999998


Q ss_pred             CCCC
Q psy6490         236 HATP  239 (398)
Q Consensus       236 ~~~~  239 (398)
                      ++..
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            8753

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

Probab=99.73  E-value=5.1e-18  Score=134.49  Aligned_cols=86  Identities=40%  Similarity=0.830  Sum_probs=80.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++||+.++..|+|+.|.|.++
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEEC
Confidence            34669999999999999999999999999999999999999999999999999999999999999899999999999999


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            876653

>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=99.73  E-value=3.7e-18  Score=131.05  Aligned_cols=84  Identities=10%  Similarity=0.212  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+++++.++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|.
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            34467999999999999999999999999999999999998899999999999999999999996 89999999999999


Q ss_pred             CCCCC
Q psy6490         236 HATPK  240 (398)
Q Consensus       236 ~~~~~  240 (398)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            87643

>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=99.73  E-value=4.6e-18  Score=133.45  Aligned_cols=84  Identities=15%  Similarity=0.263  Sum_probs=78.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|+++.++.+|.++|||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3477999999999999999999999999999999999999999999999999999999999998 899999999999998


Q ss_pred             CCCCC
Q psy6490         237 ATPKN  241 (398)
Q Consensus       237 ~~~~~  241 (398)
                      +..+.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            86544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-17  Score=130.70  Aligned_cols=84  Identities=24%  Similarity=0.360  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|++++++ +++++|||||+|.+.++|++|++ +++..|+|+.|.|.
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            34478999999999999999999999999999999999998 69999999999999999999998 89999999999999


Q ss_pred             CCCCCC
Q psy6490         236 HATPKN  241 (398)
Q Consensus       236 ~~~~~~  241 (398)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2do0_A           90 MDERAL   95 (114)
T ss_dssp             ECSCCC
T ss_pred             EcccCC
Confidence            886543

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

Probab=99.73  E-value=2.6e-17  Score=134.96  Aligned_cols=81  Identities=23%  Similarity=0.483  Sum_probs=74.3

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++++|++++.+++++|||||+|.+.++|++++ .|||..|+|+.|+|+
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            3456789999999999999999999999999999999999999999999999999988887766 699999999999999


Q ss_pred             ec
Q psy6490         324 KA  325 (398)
Q Consensus       324 ~a  325 (398)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

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

Probab=99.73  E-value=6.7e-18  Score=140.63  Aligned_cols=80  Identities=28%  Similarity=0.536  Sum_probs=75.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCC--CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFG--AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G--~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..++|||+|||+++|+++|+++|+.||  .|.+|+++.|+.+|+++|||||+|.+.++|++||+ +++..|+|+.|.|.+
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            668999999999999999999999999  99999999999999999999999999999999998 799999999999998


Q ss_pred             CCC
Q psy6490         237 ATP  239 (398)
Q Consensus       237 ~~~  239 (398)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=99.73  E-value=2.1e-17  Score=128.06  Aligned_cols=80  Identities=23%  Similarity=0.414  Sum_probs=70.6

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++|+++|+++|++||.|++|.++        +|||||+|++.++|++++ .||+..|+|+.|+|.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3457899999999999999999999999999999886        459999999988887766 5999999999999999


Q ss_pred             cCchHHHhh
Q psy6490         325 AQPKEAVQA  333 (398)
Q Consensus       325 a~~k~~~~~  333 (398)
                      +.++.....
T Consensus        80 a~~~~~~~~   88 (103)
T 2dgu_A           80 AKPPDQKRK   88 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             cCCCcccch
Confidence            988765543

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

Probab=99.73  E-value=2.5e-17  Score=124.77  Aligned_cols=82  Identities=23%  Similarity=0.412  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++++++|+++|++||.|.++++.++  +++++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            36799999999999999999999999999999999985  78899999999999999999998 8999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      .....
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            76654

>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=99.72  E-value=9.1e-18  Score=129.72  Aligned_cols=79  Identities=14%  Similarity=0.164  Sum_probs=68.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCC--ceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHF--HMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~--~~i~g~~i~v  322 (398)
                      ....++|||+|||+++++++|+++|++||.|.+|+++++      ||||||+|++.++|++++ .|++  ..|+|+.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            446789999999999999999999999999999998764      789999999988777666 4654  5699999999


Q ss_pred             EecCchHH
Q psy6490         323 KKAQPKEA  330 (398)
Q Consensus       323 ~~a~~k~~  330 (398)
                      .|++.+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99987653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=128.12  Aligned_cols=85  Identities=31%  Similarity=0.432  Sum_probs=74.4

Q ss_pred             ccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       244 ~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ......++|||+|||.++++++|+++|+.|+   .|++++++.+++++|||||+|.+.++|++|+ .||+..|+|+.|+|
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 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3445678999999999999999999999874   6778888889999999999999988887766 59999999999999


Q ss_pred             EecCchHHH
Q psy6490         323 KKAQPKEAV  331 (398)
Q Consensus       323 ~~a~~k~~~  331 (398)
                      +|++++..+
T Consensus        87 ~~a~~~~~~   95 (102)
T 2fc8_A           87 DWAKPKGEG   95 (102)
T ss_dssp             EECCCCCSS
T ss_pred             EEecCCCCC
Confidence            999887543

>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=99.72  E-value=5.4e-18  Score=142.09  Aligned_cols=135  Identities=24%  Similarity=0.315  Sum_probs=100.1

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCC-----CCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHH
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKS-----SGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYF  182 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f  182 (398)
                      ..|++++.+.+...+..+...++...............     ................++|||+|||.++++++|+++|
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F   91 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVF   91 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHHHHH
T ss_pred             ccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            45677788888888877764444221111111111100     0001111122333467999999999999999999999


Q ss_pred             hcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCC
Q psy6490         183 GMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNR  242 (398)
Q Consensus       183 ~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~  242 (398)
                      +.||.|.+|++++|+.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.++.....
T Consensus        92 ~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           92 EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             HhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            999999999999999999999999999999999999997 899999999999999876544

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=127.89  Aligned_cols=81  Identities=14%  Similarity=0.292  Sum_probs=71.4

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++|+++|+++|++||.|   +++++ .+++++|||||+|.+.++|+++++ ||+..|+|+.|+|+
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            34567899999999999999999999999987   45666 689999999999999888877765 99999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |++++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998764

>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=99.72  E-value=4.5e-18  Score=134.41  Aligned_cols=82  Identities=23%  Similarity=0.401  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +...++|||+|||.++++++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|++|+.+++..|+|+.|.|.++
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEec
Confidence            34678999999999999999999999999999999999999999999999999999999999998999999999999876


Q ss_pred             CC
Q psy6490         238 TP  239 (398)
Q Consensus       238 ~~  239 (398)
                      ..
T Consensus       102 ~~  103 (114)
T 2cq4_A          102 QA  103 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.72  E-value=3.2e-17  Score=122.22  Aligned_cols=76  Identities=14%  Similarity=0.410  Sum_probs=68.7

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-H-CCceeCCEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I-HFHMIKNKKVEC  322 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l-~~~~i~g~~i~v  322 (398)
                      .....++|||+|||.++++++|+++|++||.|.+|+++++      +|||||+|.+.++|+++++ | ++..|+|+.|+|
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            3456789999999999999999999999999999999875      7899999999888877775 7 999999999999


Q ss_pred             EecC
Q psy6490         323 KKAQ  326 (398)
Q Consensus       323 ~~a~  326 (398)
                      +|++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9984

>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=99.72  E-value=3.5e-18  Score=124.28  Aligned_cols=75  Identities=47%  Similarity=0.710  Sum_probs=71.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +|||+|||.++++++|+++|++||.|.++++.+++.+++++|||||+|.+.++|++|++.++..++|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999899999999988653

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

Probab=99.72  E-value=6.3e-18  Score=137.49  Aligned_cols=88  Identities=32%  Similarity=0.514  Sum_probs=81.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .+....++|||+|||.++|+++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            444578999999999999999999999999999999999999899999999999999999999998 8999999999999


Q ss_pred             CCCCCCCCC
Q psy6490         235 KHATPKNRP  243 (398)
Q Consensus       235 ~~~~~~~~~  243 (398)
                      .++......
T Consensus       122 ~~a~~~~~~  130 (135)
T 2lea_A          122 QMARYGRPP  130 (135)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCCCC
Confidence            998876543

>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=99.72  E-value=6e-18  Score=135.72  Aligned_cols=83  Identities=14%  Similarity=0.284  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      .....++|||+|||+++|+++|+++|+.||.|.++.++.+..+|+++|||||+|.+.++|++||++++..|+|+.|.|.+
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEE
Confidence            34467999999999999999999999999999987777777799999999999999999999999999999999999987


Q ss_pred             CCC
Q psy6490         237 ATP  239 (398)
Q Consensus       237 ~~~  239 (398)
                      +..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            753

>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=99.72  E-value=4.8e-18  Score=131.87  Aligned_cols=84  Identities=20%  Similarity=0.494  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            367899999999999999999999999999999999999899999999999999999999997 9999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      ..+..
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            76543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=2e-17  Score=129.17  Aligned_cols=78  Identities=10%  Similarity=0.166  Sum_probs=67.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G-~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ..++|||+|||+++++++|+++|++|| .|..+.|..+    .++|||||+|++.++|++|+ .|||..|+|+.|+|+++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            467899999999999999999999999 8999988533    47999999999988776666 69999999999999999


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      ....
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7654

>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=4.6e-17  Score=141.15  Aligned_cols=105  Identities=33%  Similarity=0.552  Sum_probs=85.7

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|++++.++.++|||||+|.+.++|++++++++..|+|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCchHHHhhhh--hcCCccccCCCCCC
Q psy6490         325 AQPKEAVQANL--LVGKRVILGPLGLR  349 (398)
Q Consensus       325 a~~k~~~~~~~--~~~~~~~~~~~~~~  349 (398)
                      +..+.......  ...+.++++++...
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~V~nLp~~  115 (196)
T 1l3k_A           89 AVSREDSQRPGAHLTVKKIFVGGIKED  115 (196)
T ss_dssp             CCC-----------CCSEEEEECCTTT
T ss_pred             ccCcccccccccCCCcceEEEeCCCCC
Confidence            98765443221  23355666665433

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.71  E-value=3.4e-17  Score=131.37  Aligned_cols=85  Identities=26%  Similarity=0.358  Sum_probs=79.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|++||.|.+|++.+++ +|+++|||||+|.+.++|++|++ +++..++|+.|.|.
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            44578999999999999999999999999999999999998 99999999999999999999999 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++.....
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            8876544

>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=99.71  E-value=3.3e-17  Score=126.54  Aligned_cols=80  Identities=18%  Similarity=0.223  Sum_probs=70.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CC--CcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VP--IHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~--~~~~~g~~l~v  234 (398)
                      ..++++|||+|||.++++++|+++|++||.|.+|+++++      ||||||+|.+.++|.+|++ ++  ...++|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            347799999999999999999999999999999999864      7999999999999999998 54  34599999999


Q ss_pred             CCCCCCCCC
Q psy6490         235 KHATPKNRP  243 (398)
Q Consensus       235 ~~~~~~~~~  243 (398)
                      .++..+...
T Consensus        86 ~~a~~~~~~   94 (104)
T 1wex_A           86 NYSTSKRIT   94 (104)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCcccc
Confidence            998766543

>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=99.71  E-value=3.9e-18  Score=130.11  Aligned_cols=79  Identities=9%  Similarity=0.211  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            56999999999999999999999999999999999998899999999999999999999998 89999999999998765

>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=99.71  E-value=1.7e-17  Score=129.53  Aligned_cols=81  Identities=26%  Similarity=0.377  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|+++.++ +++++|||||+|.+.++|++|++ +++..++|+.|.|.
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            33478999999999999999999999999999999999998 99999999999999999999999 89999999999988


Q ss_pred             CCC
Q psy6490         236 HAT  238 (398)
Q Consensus       236 ~~~  238 (398)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

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

Probab=99.55  E-value=5.9e-19  Score=139.94  Aligned_cols=87  Identities=18%  Similarity=0.334  Sum_probs=78.6

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE--------TVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~--------v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      ....++|||+|||.++++++|+++|++||.|.+        |+|++|+.+++++|||||+|.+.++|++|+ .||+..|+
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            345688999999999999999999999999999        899999889999999999999988877766 59999999


Q ss_pred             CEEEEEEecCchHHHh
Q psy6490         317 NKKVECKKAQPKEAVQ  332 (398)
Q Consensus       317 g~~i~v~~a~~k~~~~  332 (398)
                      |+.|+|+|+.++..+.
T Consensus        84 g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           84 GNPIKVSFATRRADFN   99 (116)
Confidence            9999999998876553

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

Probab=99.71  E-value=8.4e-18  Score=129.78  Aligned_cols=77  Identities=19%  Similarity=0.358  Sum_probs=69.7

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      ++|||+|||.++|+++|+++|++||.|++|.++++     ++|||||+|.+.++|++|+ .||+..|+|+.|+|+|++++
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            47999999999999999999999999999999877     6899999999988777766 59999999999999999887


Q ss_pred             HHH
Q psy6490         329 EAV  331 (398)
Q Consensus       329 ~~~  331 (398)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            633

>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=99.71  E-value=4e-17  Score=124.94  Aligned_cols=78  Identities=18%  Similarity=0.444  Sum_probs=69.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC--CEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK--NKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~--g~~i~v  322 (398)
                      ....++|||+|||.++|+++|+++|++||.|++|.+.++      +|||||+|.+.++|++++ .||+..|+  |+.|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345688999999999999999999999999999998754      789999999988777766 59999999  999999


Q ss_pred             EecCchH
Q psy6490         323 KKAQPKE  329 (398)
Q Consensus       323 ~~a~~k~  329 (398)
                      +|++++.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998764

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.71  E-value=8.2e-18  Score=133.59  Aligned_cols=80  Identities=18%  Similarity=0.278  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCC---EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGA---VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~---i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v  234 (398)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|++++. |+++|||||+|.+.++|++||++++..|+|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            346799999999999999999999999998   89999999986 99999999999999999999999999999999988


Q ss_pred             CCCC
Q psy6490         235 KHAT  238 (398)
Q Consensus       235 ~~~~  238 (398)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            7764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.2e-17  Score=124.83  Aligned_cols=82  Identities=16%  Similarity=0.334  Sum_probs=76.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||.++++++|+++|+.| .|.+|+++++ .+|+++|||||+|.+.++|++|+++++..++|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEEC
Confidence            3467999999999999999999999999 9999999999 6899999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy6490         238 TPKN  241 (398)
Q Consensus       238 ~~~~  241 (398)
                      ..+.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1e-17  Score=130.46  Aligned_cols=78  Identities=23%  Similarity=0.415  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      .+.++|||+|||+++|+++|+++|+.| .|.+|+|++|+. |+++|||||+|.+.++|++||++++..|+||.|.|..+.
T Consensus        14 ~~~~~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           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            356899999999999999999999999 899999999975 999999999999999999999999999999999887664

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.71  E-value=6.3e-17  Score=142.46  Aligned_cols=101  Identities=19%  Similarity=0.296  Sum_probs=84.5

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      .+.++|||+|||+++||++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++|+ .+|+..+.|+.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            35678999999999999999999999999999999999999999999999999987776655 79999999999999999


Q ss_pred             CchHHHhhhhhcCCccccCCCCCC
Q psy6490         326 QPKEAVQANLLVGKRVILGPLGLR  349 (398)
Q Consensus       326 ~~k~~~~~~~~~~~~~~~~~~~~~  349 (398)
                      ........  ....+++++++...
T Consensus        93 ~~~~~~~~--~~~~~l~v~nl~~~  114 (213)
T 4f02_A           93 QRDPSLRK--SGVGNIFIKNLDKS  114 (213)
T ss_dssp             CCCTHHHH--HCTTEEEEESCCTT
T ss_pred             cccccccc--cccccceECCcccc
Confidence            87655443  23345666665443

>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=99.71  E-value=2.3e-17  Score=131.59  Aligned_cols=78  Identities=19%  Similarity=0.347  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEE--EEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--DVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~--~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      ...++|||+|||+++|+++|+++|+.| .|+  +|+|++|+. |+++|||||+|.+.++|++||++++..|+||.|.|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            467899999999999999999999999 677  999999986 9999999999999999999999888999999999877


Q ss_pred             CC
Q psy6490         237 AT  238 (398)
Q Consensus       237 ~~  238 (398)
                      +.
T Consensus       118 a~  119 (126)
T 2hgm_A          118 SS  119 (126)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.71  E-value=2.4e-17  Score=129.09  Aligned_cols=79  Identities=20%  Similarity=0.474  Sum_probs=71.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+++      +|||||+|++.++|++|+ .|||..|+|+.|+|.|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            35678999999999999999999999999999999876      789999999988777666 79999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      +++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4g_A           97 KESPDM  102 (109)
T ss_dssp             CCCCSS
T ss_pred             CCCCCC
Confidence            887543

>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=99.71  E-value=4e-18  Score=134.93  Aligned_cols=86  Identities=19%  Similarity=0.290  Sum_probs=72.6

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.++.+..+..+++++|||||+|.+.++|++|+ .||+..|+|+.|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345789999999999999999999999999955443333347889999999999988777766 5899999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +.++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9887543

>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=99.71  E-value=7.6e-17  Score=126.21  Aligned_cols=85  Identities=16%  Similarity=0.363  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||.++|+++|+++|++||.|.+|++..+   +.++|||||+|.+.++|++|++ +++..|+|+.|.|
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            34447899999999999999999999999999999999664   4589999999999999999996 8999999999999


Q ss_pred             CCCCCCCCC
Q psy6490         235 KHATPKNRP  243 (398)
Q Consensus       235 ~~~~~~~~~  243 (398)
                      .++..+...
T Consensus        94 ~~a~~~~~~  102 (109)
T 1x4a_A           94 EFPRSGRGT  102 (109)
T ss_dssp             ECCCCCCCC
T ss_pred             EEcccCCCC
Confidence            999876543

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

Probab=99.71  E-value=2.8e-17  Score=134.72  Aligned_cols=82  Identities=32%  Similarity=0.482  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||.++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|++|++ +++..++|+.|.|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            344578999999999999999999999999999999999999999999999999999999999997 8999999999988


Q ss_pred             CCC
Q psy6490         235 KHA  237 (398)
Q Consensus       235 ~~~  237 (398)
                      .++
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=2.6e-17  Score=131.85  Aligned_cols=85  Identities=11%  Similarity=0.232  Sum_probs=72.6

Q ss_pred             CccccceeecCCCCCCCHHHHH----HHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKV  320 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~----~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i  320 (398)
                      ....++|||+||++++++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|..|+ .|||..|.|+.|
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            3456789999999999999876    6999999999987753   5788999999999977776555 799999999999


Q ss_pred             EEEecCchHHHhh
Q psy6490         321 ECKKAQPKEAVQA  333 (398)
Q Consensus       321 ~v~~a~~k~~~~~  333 (398)
                      +|.|++.+.....
T Consensus       103 ~V~~a~~~~~~~~  115 (127)
T 2a3j_A          103 VITFSETPQSQVA  115 (127)
T ss_dssp             EEEECCCCCHHHH
T ss_pred             EEEEccCcchhcc
Confidence            9999998766543

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

Probab=99.71  E-value=7.9e-18  Score=123.02  Aligned_cols=76  Identities=61%  Similarity=1.088  Sum_probs=70.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ++|||+|||.++++++|+++|++||.|.++++.+++.+++++|||||+|.+.++|++|++..+..++|+.|.|+++
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            4799999999999999999999999999999999998999999999999999999999994448899999988765

>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=99.71  E-value=3e-17  Score=129.80  Aligned_cols=82  Identities=13%  Similarity=0.243  Sum_probs=72.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|.++++   +.++|||||+|.+.++|.+|+ .|||..|+|+.|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45678999999999999999999999999999999876   455999999999988777766 59999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      .++...
T Consensus        83 ~~~~~~   88 (115)
T 3lqv_A           83 NANRAF   88 (115)
T ss_dssp             CHHHHT
T ss_pred             cCChhh
Confidence            876543

>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=99.71  E-value=1.3e-17  Score=130.07  Aligned_cols=82  Identities=13%  Similarity=0.223  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC---EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGA---VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID  233 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~---i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~  233 (398)
                      +....++|||+|||+++|+++|+++|+.||.   |.+|+|++++. |+++|||||+|.+.++|++||++++..++|+.|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEE
Confidence            3347799999999999999999999999998   89999999986 9999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy6490         234 PKHATP  239 (398)
Q Consensus       234 v~~~~~  239 (398)
                      |.++..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            988754

>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=99.70  E-value=3.5e-17  Score=122.97  Aligned_cols=77  Identities=32%  Similarity=0.581  Sum_probs=62.9

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCce--eCCEEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHM--IKNKKVECK  323 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~--i~g~~i~v~  323 (398)
                      .....+|||+|||+++|+++|+++|++||.|++|+|+++     +||||||+|++.++|++   +++..  ++|+.|.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS---LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEE
Confidence            345678999999999999999999999999999999875     69999999999888874   45554  569999999


Q ss_pred             ecCchHH
Q psy6490         324 KAQPKEA  330 (398)
Q Consensus       324 ~a~~k~~  330 (398)
                      ++.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9998764

>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=99.70  E-value=2.1e-17  Score=133.00  Aligned_cols=86  Identities=15%  Similarity=0.302  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ...+.++|||+|||.++|+++|+++|+.||.|.+|+|+.++.++.++|||||+|.+.++|++|++ +++..|+|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            33467999999999999999999999999999999999999999999999999999999999997 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++..+..
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            8875543

>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=99.70  E-value=2.5e-17  Score=128.18  Aligned_cols=78  Identities=12%  Similarity=0.204  Sum_probs=67.5

Q ss_pred             CccccceeecCCCCC-CCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HH--CCceeCCEEEE
Q psy6490         246 GNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EI--HFHMIKNKKVE  321 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~-~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l--~~~~i~g~~i~  321 (398)
                      ....++|||+|||++ +++++|+++|++||.|.+|+|+++      ||||||+|++.++|++|+ .|  ++..|+||.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456789999999998 999999999999999999999743      799999999988776665 46  45679999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |.|+..+.
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99997664

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.70  E-value=2.7e-17  Score=127.77  Aligned_cols=80  Identities=14%  Similarity=0.206  Sum_probs=70.6

Q ss_pred             ccccceeecCCCCCC------CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCE-
Q psy6490         247 NRTKKIFVGGVSQDT------SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNK-  318 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~------tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~-  318 (398)
                      ...++|||+|||+.+      ++++|+++|++||.|.+|.|.  +.+|+++|||||+|.+.++|.+|+ .|||..|+|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            346789999999999      789999999999999999988  368899999999999977666555 6999999999 


Q ss_pred             EEEEEecCch
Q psy6490         319 KVECKKAQPK  328 (398)
Q Consensus       319 ~i~v~~a~~k  328 (398)
                      .|+|.|+...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999999754

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.70  E-value=2.4e-17  Score=128.71  Aligned_cols=80  Identities=14%  Similarity=0.145  Sum_probs=69.8

Q ss_pred             cceeecCC----CCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-----HHH---HHHH-H--HHCCce
Q psy6490         250 KKIFVGGV----SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-----EEV---VDHI-C--EIHFHM  314 (398)
Q Consensus       250 ~~l~V~nL----p~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-----~ea---a~a~-~--~l~~~~  314 (398)
                      ..|||+||    ++.+++++|+++|+.||+|.+|.++.|+.||+++|||||+|.|     .++   |.++ .  +++|..
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            57999999    9999999999999999999999999999999999999999995     232   4444 4  479999


Q ss_pred             eCCEEEEEEecCchH
Q psy6490         315 IKNKKVECKKAQPKE  329 (398)
Q Consensus       315 i~g~~i~v~~a~~k~  329 (398)
                      |+||.|+|.+-+...
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999976543

>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=99.70  E-value=4e-17  Score=127.80  Aligned_cols=83  Identities=22%  Similarity=0.381  Sum_probs=77.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCC-EEEEEEe-eCCCCCCcccEEEEEEcChHhHHHHHh-CC--CcccCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIM-KDPITQRSRGFGFITFAEPETVEKVLK-VP--IHTLDGKKIDP  234 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~-i~~~~~~-~~~~~~~~~g~afV~f~~~e~a~~al~-~~--~~~~~g~~l~v  234 (398)
                      +.++|||+|||.++++++|+++|+.||. |.+|+++ .++.++.++|||||+|.+.++|++|++ ++  +..++|+.|.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            6799999999999999999999999998 9999998 888889999999999999999999999 65  48899999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++..+..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99987654

>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=99.70  E-value=5.1e-17  Score=124.70  Aligned_cols=81  Identities=20%  Similarity=0.247  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C--CCcccCCcccC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V--PIHTLDGKKID  233 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~--~~~~~~g~~l~  233 (398)
                      ...++++|||+|||.++++++|+++|+.||.|.+|+++++      ||||||+|.+.++|.+|++ +  ++..++|+.|.
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            3347899999999999999999999999999999998875      8999999999999999998 3  56779999999


Q ss_pred             CCCCCCCCCC
Q psy6490         234 PKHATPKNRP  243 (398)
Q Consensus       234 v~~~~~~~~~  243 (398)
                      |.++..+...
T Consensus        85 V~~a~~~~~~   94 (101)
T 2cq1_A           85 IQYSNHKELK   94 (101)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEcCcccCc
Confidence            9999866543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.70  E-value=2.7e-17  Score=131.90  Aligned_cols=82  Identities=18%  Similarity=0.455  Sum_probs=77.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++|+++++..|+|+.|.|.++..
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            56899999999999999999999999999999999999899999999999999999999999999999999999998875


Q ss_pred             CC
Q psy6490         240 KN  241 (398)
Q Consensus       240 ~~  241 (398)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.70  E-value=1.4e-17  Score=127.75  Aligned_cols=77  Identities=17%  Similarity=0.239  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCC--cccCCcccCCC
Q psy6490         160 TSAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPI--HTLDGKKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~--~~~~g~~l~v~  235 (398)
                      ++++|||+|||+ ++|+++|+++|+.||.|.+|+|+++      +|||||+|.+.++|.+|++ +++  ..|+|++|.|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            689999999999 9999999999999999999999876      6899999999999999998 554  45999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++.....
T Consensus        88 ~a~~~~~   94 (102)
T 1x4d_A           88 LSQKYKR   94 (102)
T ss_dssp             EECCCTT
T ss_pred             ECCCCCC
Confidence            9876544

>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=99.70  E-value=7.3e-17  Score=126.06  Aligned_cols=77  Identities=18%  Similarity=0.298  Sum_probs=69.3

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC-----EEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN-----KKV  320 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g-----~~i  320 (398)
                      ...++|||+|||+++|+++|+++|++||.|++|.|+++       |||||+|++.++|++|+ +||+..|+|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45688999999999999999999999999999999876       79999999987776666 599999999     999


Q ss_pred             EEEecCchHH
Q psy6490         321 ECKKAQPKEA  330 (398)
Q Consensus       321 ~v~~a~~k~~  330 (398)
                      +|+++.++..
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9999988653

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

Probab=99.70  E-value=3.3e-17  Score=126.44  Aligned_cols=75  Identities=11%  Similarity=0.299  Sum_probs=67.4

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++++++|+++|++||.|++|++.      +++|||||+|.+.++|++++ .|||..|+|+.|+|+|++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46789999999999999999999999999999987      34899999999977776655 799999999999999997


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.70  E-value=1.3e-17  Score=135.25  Aligned_cols=80  Identities=16%  Similarity=0.272  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCC---EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGA---VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~---i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v  234 (398)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++||++++..|+||.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            346799999999999999999999999999   89999999986 99999999999999999999999999999999998


Q ss_pred             CCCC
Q psy6490         235 KHAT  238 (398)
Q Consensus       235 ~~~~  238 (398)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8764

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

Probab=99.70  E-value=4.7e-17  Score=127.02  Aligned_cols=79  Identities=25%  Similarity=0.400  Sum_probs=69.1

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++|+++|+++|++||.|++|.++        +|||||+|.+.++|++++ .|||..|+|+.|+|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999987        789999999988777666 599999999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |++++..+
T Consensus        99 ~a~~~~~r  106 (108)
T 2jvo_A           99 YSKLPAKR  106 (108)
T ss_dssp             SCSCCC--
T ss_pred             EecCCCCC
Confidence            99876543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.70  E-value=4.2e-17  Score=120.43  Aligned_cols=73  Identities=16%  Similarity=0.319  Sum_probs=67.1

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCc-cc
Q psy6490         161 SAKLFVGGLSWQT------SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGK-KI  232 (398)
Q Consensus       161 ~~~l~v~nLp~~~------t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~-~l  232 (398)
                      +++|||+|||.++      ++++|+++|++||.|.++++.+  .+|+++|||||+|.+.++|++|++ +++..++|+ .|
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 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3799999999999      7799999999999999999873  588999999999999999999998 899999999 88


Q ss_pred             CCC
Q psy6490         233 DPK  235 (398)
Q Consensus       233 ~v~  235 (398)
                      .|.
T Consensus        79 ~V~   81 (81)
T 2krb_A           79 RVN   81 (81)
T ss_dssp             CCC
T ss_pred             EeC
Confidence            763

>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=99.70  E-value=7e-18  Score=127.30  Aligned_cols=80  Identities=30%  Similarity=0.613  Sum_probs=72.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      ++|||+|||.++++++|+++|+.||.|.++++.+++.+|+++|||||+|.+.+ |.+|++ +++..++|+.|.|+++...
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            68999999999999999999999999999999999999999999999999999 999998 8999999999999998765


Q ss_pred             CC
Q psy6490         241 NR  242 (398)
Q Consensus       241 ~~  242 (398)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>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=99.70  E-value=1.7e-17  Score=124.52  Aligned_cols=81  Identities=21%  Similarity=0.494  Sum_probs=75.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCC-cccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR-SRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~-~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ..++|||+|||.++++++|+++|+.||.|.++++..++.++. ++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            568999999999999999999999999999999999987766 89999999999999999999 8999999999999887


Q ss_pred             CCC
Q psy6490         238 TPK  240 (398)
Q Consensus       238 ~~~  240 (398)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=2.2e-17  Score=129.70  Aligned_cols=85  Identities=24%  Similarity=0.386  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH---HHHhcCCCEEEEEEeeCCCCC---CcccEEEEEEcChHhHHHHHh-CCCcccCCc
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLR---EYFGMFGAVTDVLIMKDPITQ---RSRGFGFITFAEPETVEKVLK-VPIHTLDGK  230 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~---~~f~~~G~i~~~~~~~~~~~~---~~~g~afV~f~~~e~a~~al~-~~~~~~~g~  230 (398)
                      ....++|||+|||.++++++|+   ++|++||.|.+|++.+++.++   +++|||||+|.+.++|++|++ +++..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3467899999999999999999   999999999999999988654   466999999999999999999 799999999


Q ss_pred             ccCCCCCCCCCC
Q psy6490         231 KIDPKHATPKNR  242 (398)
Q Consensus       231 ~l~v~~~~~~~~  242 (398)
                      .|.|.++..+..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999987653

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

Probab=99.70  E-value=3.5e-17  Score=123.43  Aligned_cols=77  Identities=21%  Similarity=0.543  Sum_probs=69.4

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|++||.|++|++.        +|||||+|++.++|++++ .||+..|+|+.|+|+|
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            3467899999999999999999999999999999986        679999999988887766 6999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      ++++..
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987654

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

Probab=99.70  E-value=1.9e-17  Score=129.58  Aligned_cols=84  Identities=29%  Similarity=0.591  Sum_probs=76.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .......++|||+|||.++++++|+++|++||.|.+|++.+++  +.++|||||+|.+.++|++|++ +++..++|+.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3445578999999999999999999999999999999999985  4589999999999999999998 899999999999


Q ss_pred             CCCCCCC
Q psy6490         234 PKHATPK  240 (398)
Q Consensus       234 v~~~~~~  240 (398)
                      |.++..+
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9988754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.70  E-value=4.1e-17  Score=126.80  Aligned_cols=85  Identities=16%  Similarity=0.270  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCC------CHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC
Q psy6490         156 GDDPTSAKLFVGGLSWQT------SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD  228 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~------t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~  228 (398)
                      ......++|||+|||.++      ++++|+++|++||.|.+|++.  +.+|+++|||||+|.+.++|.+|++ +++..++
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   87 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC
Confidence            344467899999999999      789999999999999999998  3588999999999999999999999 8999999


Q ss_pred             Cc-ccCCCCCCCCCC
Q psy6490         229 GK-KIDPKHATPKNR  242 (398)
Q Consensus       229 g~-~l~v~~~~~~~~  242 (398)
                      |+ .|.|.++....+
T Consensus        88 g~~~l~V~~a~~~~k  102 (105)
T 2nlw_A           88 KQHTFRVNLFTDFDK  102 (105)
T ss_dssp             TTCEEEEECSCCCCC
T ss_pred             CCceEEEEEcchHhh
Confidence            98 999998875443

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

Probab=99.70  E-value=2.4e-17  Score=125.21  Aligned_cols=77  Identities=17%  Similarity=0.252  Sum_probs=69.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCc--ccCCcccCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIH--TLDGKKIDPK  235 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~--~~~g~~l~v~  235 (398)
                      .++++|||+|||.++|+++|+++|++||.|.+++++++      ||||||+|.+.++|.+|++ +++.  .++|++|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            37899999999999999999999999999999999863      8999999999999999998 5554  4889999999


Q ss_pred             CCCCCC
Q psy6490         236 HATPKN  241 (398)
Q Consensus       236 ~~~~~~  241 (398)
                      +++.+.
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            987654

>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=99.69  E-value=1.1e-16  Score=122.45  Aligned_cols=75  Identities=21%  Similarity=0.411  Sum_probs=67.3

Q ss_pred             CccccceeecCCCC-CCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         246 GNRTKKIFVGGVSQ-DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       246 ~~~~~~l~V~nLp~-~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      ....++|||+|||. ++++++|+++|+.||.|.+|++.        +|||||+|++.++|++++ .|||..|+|+.|+|+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44678999999998 99999999999999999999882        789999999988777666 599999999999999


Q ss_pred             ecCch
Q psy6490         324 KAQPK  328 (398)
Q Consensus       324 ~a~~k  328 (398)
                      |++++
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99765

>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=99.69  E-value=4.3e-17  Score=128.27  Aligned_cols=81  Identities=19%  Similarity=0.263  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CC--CcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VP--IHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~--~~~~~g~~l~v  234 (398)
                      ..++++|||+|||+++|+++|+++|+.||.|.+|+|+++      ||||||+|.+.++|++|++ ++  +..++|+.|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            346799999999999999999999999999999999876      8999999999999999998 44  35799999999


Q ss_pred             CCCCCCCCCc
Q psy6490         235 KHATPKNRPK  244 (398)
Q Consensus       235 ~~~~~~~~~~  244 (398)
                      .++..+....
T Consensus       102 ~~a~~k~~~~  111 (119)
T 2ad9_A          102 QFSNHKELKT  111 (119)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCCCCCc
Confidence            9988765543

>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=99.69  E-value=3.5e-17  Score=125.01  Aligned_cols=80  Identities=18%  Similarity=0.176  Sum_probs=74.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHH----HHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLR----EYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~----~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      +.++|||+|||.++++++|+    ++|++||.|.+|+++.++.+   +|||||+|.+.++|++|++ +++..++|+.|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            66899999999999999999    99999999999999998765   8899999999999999998 9999999999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++.....
T Consensus        85 ~~a~~~~~   92 (96)
T 2dgx_A           85 SLATGASG   92 (96)
T ss_dssp             EECCCSSC
T ss_pred             EEcCCCCC
Confidence            99876544

>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=99.69  E-value=1e-16  Score=126.49  Aligned_cols=75  Identities=21%  Similarity=0.407  Sum_probs=68.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcc
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKK  231 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~  231 (398)
                      ..+...++|||+|||.++++++|+++|+.||.|.+|++++++ ++.++|||||+|.+.++|++|++ +++..++++.
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~   95 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPP   95 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCT
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCc
Confidence            334577999999999999999999999999999999999998 99999999999999999999998 8888885444

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=1.2e-17  Score=123.35  Aligned_cols=71  Identities=15%  Similarity=0.276  Sum_probs=64.1

Q ss_pred             cceeecCCCCCC------CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCE-EEE
Q psy6490         250 KKIFVGGVSQDT------SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNK-KVE  321 (398)
Q Consensus       250 ~~l~V~nLp~~~------tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~-~i~  321 (398)
                      ++|||+|||..+      ++++|+++|++||.|.+|++.  +.+|+++|||||+|.+.++|++|+ .|||..|+|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      779999999999999999987  358899999999999988777766 5999999999 887


Q ss_pred             E
Q psy6490         322 C  322 (398)
Q Consensus       322 v  322 (398)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.69  E-value=5.8e-17  Score=135.43  Aligned_cols=86  Identities=22%  Similarity=0.386  Sum_probs=80.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++|+++|+++|++||.|.+|+|+.++.++.++|||||+|.+.++|++||+ +++..|+|+.|.|.
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            33477999999999999999999999999999999999999999999999999999999999999 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++.....
T Consensus       115 ~a~~~~~  121 (156)
T 1h2v_Z          115 WDAGFKE  121 (156)
T ss_dssp             EESCCCT
T ss_pred             ECCCCCC
Confidence            9876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=9e-17  Score=121.70  Aligned_cols=78  Identities=21%  Similarity=0.379  Sum_probs=69.0

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|.+++        +||||+|++.++|++++ .||+..|+|+.|+|+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            345678999999999999999999999999999999873        49999999987776666 699999999999999


Q ss_pred             ecCchHH
Q psy6490         324 KAQPKEA  330 (398)
Q Consensus       324 ~a~~k~~  330 (398)
                      |++++..
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9987643

>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=99.69  E-value=2.6e-17  Score=125.99  Aligned_cols=82  Identities=18%  Similarity=0.372  Sum_probs=72.7

Q ss_pred             ccccceeecCCCCCCCHHHHH----HHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~----~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      ...++|||+|||.++++++|+    ++|++||.|.+|.+.+   ++.++|||||+|.+.++|++++ .|||..|+|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            457899999999999999999    9999999999998873   4678999999999988776666 5999999999999


Q ss_pred             EEecCchHHH
Q psy6490         322 CKKAQPKEAV  331 (398)
Q Consensus       322 v~~a~~k~~~  331 (398)
                      |.|++++...
T Consensus        83 v~~a~~~~~~   92 (97)
T 1nu4_A           83 IQYAKTDSDI   92 (97)
T ss_dssp             EEECSSCCTH
T ss_pred             EEEccCCCcc
Confidence            9999887644

>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=99.69  E-value=7.7e-17  Score=123.86  Aligned_cols=79  Identities=24%  Similarity=0.496  Sum_probs=70.1

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++++++|+++|++||.|++|++.++      +|||||+|++.++|++++ .||+..|+|+.|+|.
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            3456789999999999999999999999999999998755      789999999977776655 799999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |++++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998754

>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=99.69  E-value=1.6e-17  Score=134.99  Aligned_cols=83  Identities=16%  Similarity=0.223  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||+++|+++|+++|+.|| |++|+|++|+. ++++|||||+|.+.++|++||++++..|+|+.|.|..+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEEC
Confidence            34678999999999999999999999999 77999999985 99999999999999999999999999999999999887


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      .....
T Consensus       121 ~~~~~  125 (139)
T 2hgn_A          121 STTGA  125 (139)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            76543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=6.5e-17  Score=124.75  Aligned_cols=83  Identities=24%  Similarity=0.426  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .+...++|||+|||.++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|++ +++..|+|+.|.|.
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            44578999999999999999999999999977   56666 588999999999999999999998 99999999999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      ++..+...
T Consensus        87 ~a~~~~~~   94 (101)
T 2fc9_A           87 LQGPRGSP   94 (101)
T ss_dssp             ECSSCCCC
T ss_pred             EcCCCCCC
Confidence            98876543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=4.1e-17  Score=124.61  Aligned_cols=79  Identities=15%  Similarity=0.238  Sum_probs=69.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|+.||.|..+     ..++.++|||||+|.+.++|+++++ |||..|+|+.|+|.|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4467899999999999999999999999988765     3578899999999999888877665 999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      +.++.
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            98764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=1.6e-17  Score=128.49  Aligned_cols=81  Identities=30%  Similarity=0.588  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|++++++ +|+++|||||+|.+.++|++|++ ++..++|+.|.|.++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECC
Confidence            367999999999999999999999999999999999998 99999999999999999999999 8889999999988776


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      .+.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=8.8e-17  Score=123.02  Aligned_cols=79  Identities=11%  Similarity=0.255  Sum_probs=68.7

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++++++|+++|+.||.|. ++++.+    .++|||||+|.+.++|++++ .|||..|+|+.|+|+|
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34567999999999999999999999999997 666654    56899999999987776665 7999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      ++++.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98763

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.4e-16  Score=122.32  Aligned_cols=77  Identities=23%  Similarity=0.382  Sum_probs=68.3

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhc--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQF--GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~--G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      .....++|||+|||.++|+++|+++|++|  |.|.+|.+.        +|||||+|.+.++|++++ .||+..|+|+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34567899999999999999999999999  999988764        679999999988777766 5999999999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |.|++++.
T Consensus        83 v~~a~~~~   90 (99)
T 2cpd_A           83 VTLAKPVD   90 (99)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99998764

>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=99.69  E-value=1.9e-16  Score=133.45  Aligned_cols=96  Identities=19%  Similarity=0.372  Sum_probs=82.9

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      .++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|++++ .++|..++|+.|+|.|+.+
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            578999999999999999999999999999999999889999999999999988887777 5999999999999999987


Q ss_pred             hHHHhhhhhcCCccccCCCCC
Q psy6490         328 KEAVQANLLVGKRVILGPLGL  348 (398)
Q Consensus       328 k~~~~~~~~~~~~~~~~~~~~  348 (398)
                      +...    ...+.++++++..
T Consensus        82 ~~~~----~~~~~l~v~nl~~   98 (167)
T 1fxl_A           82 SSAS----IRDANLYVSGLPK   98 (167)
T ss_dssp             CCGG----GTTCEEEEESCCT
T ss_pred             Cccc----CCCCcEEECCCCC
Confidence            6543    2334556655543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.68  E-value=8.6e-18  Score=129.73  Aligned_cols=84  Identities=26%  Similarity=0.379  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+ .++.+..+++++|||||+|.+.++|++|+++++..++|+.|.|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            346789999999999999999999999999888 6677777889999999999999999999999999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      ..+..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76554

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.68  E-value=4.5e-17  Score=119.18  Aligned_cols=72  Identities=17%  Similarity=0.183  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+..|||+||++.+||++|+++|.+||+|.++++..      +||||||+|.+.++|++|++ +|+..+.|+.|+|+.+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            568999999999999999999999999999999965      59999999999999999999 8999999999988777

>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=99.68  E-value=1.1e-16  Score=122.91  Aligned_cols=80  Identities=29%  Similarity=0.485  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ...+.++|||+|||.++++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++ +++..++|+.|.|.
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            3447799999999999999999999999999999999864      7999999999999999997 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++..+..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpj_A           85 FACHSAS   91 (99)
T ss_dssp             ESSCCSC
T ss_pred             EcCCCCC
Confidence            9877654

>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=99.68  E-value=3.7e-17  Score=124.12  Aligned_cols=78  Identities=15%  Similarity=0.335  Sum_probs=66.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCC-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCC-ceeCCEEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGK-VEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHF-HMIKNKKVECK  323 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~-i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~-~~i~g~~i~v~  323 (398)
                      ...++|||+|||.++|+++|+++|++||. |..+.+ .      ++|||||+|.+.++|++++ +||+ ..|+|+.|+|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-L------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-E------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-c------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45688999999999999999999999999 665555 2      4789999999988776666 6999 99999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |+.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99877543

>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=99.68  E-value=6.6e-17  Score=143.45  Aligned_cols=80  Identities=20%  Similarity=0.464  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCC--CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFG--AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G--~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..++|||+||++++|+++|+++|++||  .|++|+|++|+.++++||||||+|.+.++|++||+ +++..|+|+.|.|.+
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            678999999999999999999999999  99999999999999999999999999999999999 899999999999988


Q ss_pred             CCC
Q psy6490         237 ATP  239 (398)
Q Consensus       237 ~~~  239 (398)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            753

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

Probab=99.68  E-value=1.9e-16  Score=119.32  Aligned_cols=76  Identities=25%  Similarity=0.426  Sum_probs=68.0

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++|+++|+++|++||.|.+|++++        +||||+|.+.++|++++ .||+..|+|+.|+|.|
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999873        49999999988777666 5999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      +.++.
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98764

>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=99.68  E-value=1.4e-16  Score=118.78  Aligned_cols=76  Identities=25%  Similarity=0.473  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C-CCcccCCcccCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V-PIHTLDGKKIDP  234 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~-~~~~~~g~~l~v  234 (398)
                      .+...++|||+|||.++++++|+++|++||.|.++++.++      +|||||+|.+.++|++|++ + ++..++|+.|.|
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            3457899999999999999999999999999999999874      8999999999999999998 7 889999999999


Q ss_pred             CCCC
Q psy6490         235 KHAT  238 (398)
Q Consensus       235 ~~~~  238 (398)
                      .+++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            8763

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=3.8e-17  Score=130.04  Aligned_cols=78  Identities=22%  Similarity=0.383  Sum_probs=71.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCE----EEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAV----TDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i----~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~  235 (398)
                      +.++|||+|||+++|+++|+++|+.||.|    .+|+|+.++ +|+++|||||+|.+.++|++||+.++..|+||.|.|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            67899999999999999999999999975    689999985 8999999999999999999999999999999998887


Q ss_pred             CCC
Q psy6490         236 HAT  238 (398)
Q Consensus       236 ~~~  238 (398)
                      .+.
T Consensus       101 ~a~  103 (123)
T 2dha_A          101 RST  103 (123)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            654

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

Probab=99.68  E-value=8.3e-17  Score=122.42  Aligned_cols=79  Identities=19%  Similarity=0.412  Sum_probs=69.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||+++|+++|+++|+.||.|.+|  +.++.+++   ||||+|.+.++|+++++||+..|+|+.|+|+++.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECC
Confidence            345789999999999999999999999999987  56655664   9999999999888888899999999999999987


Q ss_pred             chHH
Q psy6490         327 PKEA  330 (398)
Q Consensus       327 ~k~~  330 (398)
                      .+..
T Consensus        81 ~~~~   84 (94)
T 2e5g_A           81 QKEF   84 (94)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            6643

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

Probab=99.68  E-value=1.3e-16  Score=135.71  Aligned_cols=83  Identities=14%  Similarity=0.235  Sum_probs=75.7

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||+++++++|+++|+.||.|++|.|+.+. ++.++|||||+|++.++|++|+ +||+..|+|+.|+|.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999997 8999999999999988777666 5999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            98654

>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=99.67  E-value=2.2e-16  Score=136.43  Aligned_cols=117  Identities=15%  Similarity=0.240  Sum_probs=89.8

Q ss_pred             ChHhHHHHHh-C--CCcccCCcccCCCCCCCCCCCc------cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEe
Q psy6490         212 EPETVEKVLK-V--PIHTLDGKKIDPKHATPKNRPK------IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML  282 (398)
Q Consensus       212 ~~e~a~~al~-~--~~~~~~g~~l~v~~~~~~~~~~------~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~  282 (398)
                      +.+....|++ .  ....+.+....+........+.      .....++|||+|||+++|+++|+++|+.||.|.+|+|.
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            4566677776 3  3344555544444442222111      12246789999999999999999999999999999999


Q ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCchH
Q psy6490         283 MDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       283 ~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      ++. ++.++|||||+|++.++|++|+++.+..|+|+.|+|.|+..-.
T Consensus       143 ~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          143 RTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYF  188 (193)
T ss_dssp             ECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC-
T ss_pred             ECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHHH
Confidence            985 5899999999999999999998877789999999999987543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.5e-16  Score=121.75  Aligned_cols=81  Identities=15%  Similarity=0.297  Sum_probs=71.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ......++|||+|||.++++++|+++|+.||.|. ++++.+    .++|||||+|.+.++|++|++ +++..++|+.|.|
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3344679999999999999999999999999997 666654    479999999999999999997 8999999999999


Q ss_pred             CCCCCCC
Q psy6490         235 KHATPKN  241 (398)
Q Consensus       235 ~~~~~~~  241 (398)
                      .++..+.
T Consensus        89 ~~a~~~~   95 (97)
T 2e5j_A           89 ALARQQR   95 (97)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9987654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=1.3e-16  Score=127.75  Aligned_cols=81  Identities=15%  Similarity=0.269  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH----HHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLR----EYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~----~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      ..++++|||+||+.++++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|.+|++ +++..+.|+.|
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            3467899999999999999876    6999999999988754   57889999999999999999997 99999999999


Q ss_pred             CCCCCCCCC
Q psy6490         233 DPKHATPKN  241 (398)
Q Consensus       233 ~v~~~~~~~  241 (398)
                      .|.++..+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999987654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.1e-16  Score=123.60  Aligned_cols=86  Identities=33%  Similarity=0.456  Sum_probs=76.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       155 ~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .......++|||+|||.++++++|+++|+.|+   +++++.++.+++++|||||+|.+.++|++||+ +++..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34455789999999999999999999999873   67888888899999999999999999999998 899999999999


Q ss_pred             CCCCCCCCCC
Q psy6490         234 PKHATPKNRP  243 (398)
Q Consensus       234 v~~~~~~~~~  243 (398)
                      |.++..+...
T Consensus        86 V~~a~~~~~~   95 (102)
T 2fc8_A           86 LDWAKPKGEG   95 (102)
T ss_dssp             EEECCCCCSS
T ss_pred             EEEecCCCCC
Confidence            9999876553

>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=99.67  E-value=2.3e-16  Score=120.67  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC--CcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD--GKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~--g~~l~v  234 (398)
                      ....++|||+|||.++++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++ +++..++  |+.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            346799999999999999999999999999999999764      7899999999999999998 8999999  999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++..+..
T Consensus        88 ~~a~~~~~   95 (97)
T 1why_A           88 DFAKSGPS   95 (97)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99876543

>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=99.67  E-value=1.5e-16  Score=131.59  Aligned_cols=79  Identities=13%  Similarity=0.186  Sum_probs=68.3

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC--EEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN--KKVECK  323 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v~  323 (398)
                      ....+|||+||++.+|+++|+++|++||.|++|+|..+    .++|||||+|++.++|++++ .|||..|.|  +.|+|+
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 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34567999999999999999999999999999998654    25799999999977776555 699999965  999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |++++.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            999874

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

Probab=99.67  E-value=2.9e-16  Score=118.37  Aligned_cols=77  Identities=22%  Similarity=0.521  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|++.        +|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            378999999999999999999999999999999996        6799999999999999997 8999999999999999


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus        78 ~~~~~~   83 (90)
T 2dnq_A           78 KNKSKA   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876653

>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=5.8e-17  Score=136.48  Aligned_cols=125  Identities=22%  Similarity=0.324  Sum_probs=106.0

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      ..++++..+.+...+..+...+++....+....+........      ......++|||+|||.++++++|+++|+.||.
T Consensus        40 ~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~  113 (166)
T 3md3_A           40 NVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPS  113 (166)
T ss_dssp             CEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTT
T ss_pred             CCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC------CCCCCCceEEECCCCCCCCHHHHHHHHhccCC
Confidence            456788999999999988877777666666555554432221      23346789999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      |.++++.++..+|.++|||||+|.+.++|.+|++ +++..++|+.|.|.++.
T Consensus       114 i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          114 YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             eeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            9999999999899999999999999999999998 89999999999998875

>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=99.67  E-value=7.8e-17  Score=126.44  Aligned_cols=75  Identities=15%  Similarity=0.160  Sum_probs=67.0

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||+++++++|+++|++||.|.+|.|.+      ++|||||+|.+.++|++|+ .|||..|+|+.|+|.|+.
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            467899999999999999999999999999998864      4789999999987776655 699999999999999987


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.67  E-value=1.9e-16  Score=137.50  Aligned_cols=134  Identities=16%  Similarity=0.221  Sum_probs=109.4

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCC------------CCCCCCCCCcEEEEcCCCCCCCH
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRS------------TPTGDDPTSAKLFVGGLSWQTSS  175 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~l~v~nLp~~~t~  175 (398)
                      ..+++|+.+.+...+..++ .+++....+....+...........            .........++|||+|||.++++
T Consensus        50 ~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  128 (198)
T 2yh0_A           50 DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLND  128 (198)
T ss_dssp             TTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCH
T ss_pred             CCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCH
Confidence            3578899999999999998 7777766666666554432211110            11122357799999999999999


Q ss_pred             HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCCC
Q psy6490         176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNR  242 (398)
Q Consensus       176 ~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~~  242 (398)
                      ++|+++|++||.|.++++.+++.+|.++|||||+|.+.++|.+|++ +++..++|+.|.|.++.++..
T Consensus       129 ~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             HHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             HHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999999999999999999999899999999999999999999998 899999999999999877654

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

Probab=99.66  E-value=1.9e-16  Score=122.08  Aligned_cols=74  Identities=15%  Similarity=0.323  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|++||.|.++++.+      ++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            568999999999999999999999999999999983      58999999999999999997 89999999999999987


Q ss_pred             C
Q psy6490         239 P  239 (398)
Q Consensus       239 ~  239 (398)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.66  E-value=1.2e-16  Score=135.53  Aligned_cols=120  Identities=18%  Similarity=0.252  Sum_probs=103.4

Q ss_pred             CCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCE
Q psy6490         109 SGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAV  188 (398)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i  188 (398)
                      .++++..+.+...+..++ .+++....+....+......        ......++|||+|||.++++++|+++|++||.|
T Consensus        51 ~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~--------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v  121 (172)
T 2g4b_A           51 KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY--------QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPL  121 (172)
T ss_dssp             TTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSC--------CCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCccc--------CCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCc
Confidence            578899999999999998 77777666666665543222        122357999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         189 TDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       189 ~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .++++.+++.+|.++|||||+|.+.++|.+|++ +++..++|+.|.|.++
T Consensus       122 ~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          122 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             EEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             eEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            999999999899999999999999999999998 8999999999998876

>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=99.66  E-value=2.1e-16  Score=133.37  Aligned_cols=96  Identities=20%  Similarity=0.326  Sum_probs=82.6

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++++++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|++++ .+++..++|+.|+|.|+.
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            4578999999999999999999999999999999999889999999999999988887777 599999999999999998


Q ss_pred             chHHHhhhhhcCCccccCCCC
Q psy6490         327 PKEAVQANLLVGKRVILGPLG  347 (398)
Q Consensus       327 ~k~~~~~~~~~~~~~~~~~~~  347 (398)
                      ++...    ...+.++++++.
T Consensus        82 ~~~~~----~~~~~l~v~nl~   98 (168)
T 1b7f_A           82 PGGES----IKDTNLYVTNLP   98 (168)
T ss_dssp             CCSST----TTTCEEEEESCC
T ss_pred             CCccc----CCCCCEEEeCCC
Confidence            76533    223445555543

>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=99.66  E-value=3.3e-16  Score=122.27  Aligned_cols=77  Identities=19%  Similarity=0.303  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC-----ccc
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG-----KKI  232 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g-----~~l  232 (398)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+.+       |||||+|.+.++|++||+ +++..|+|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            36799999999999999999999999999999999876       799999999999999999 99999999     999


Q ss_pred             CCCCCCCCCC
Q psy6490         233 DPKHATPKNR  242 (398)
Q Consensus       233 ~v~~~~~~~~  242 (398)
                      .|.++..+..
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9998877554

>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=99.66  E-value=4e-17  Score=134.34  Aligned_cols=86  Identities=15%  Similarity=0.272  Sum_probs=70.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEE--E---eecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--M---LMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKK  319 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~--i---~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~  319 (398)
                      ....++|||+|||+++|+++|+++|+.||.|..+.  +   ++...+++++|||||+|.+.++|.+|+ .|||..|+|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            34568899999999999999999999999988751  1   111247889999999999988777666 59999999999


Q ss_pred             EEEEecCchHHH
Q psy6490         320 VECKKAQPKEAV  331 (398)
Q Consensus       320 i~v~~a~~k~~~  331 (398)
                      |+|.|+++...+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999775433

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

Probab=99.66  E-value=1.9e-16  Score=120.84  Aligned_cols=79  Identities=15%  Similarity=0.217  Sum_probs=69.1

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEE-EeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV-MLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~-i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ...++|||+|||+++++++|+++|++||.|.+|+ |++++.++    .|||+|.+.++|++++ .|||..|+|+.|+|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3568899999999999999999999999999994 87776543    4999999988776666 6999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      +.+++
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            98874

>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=99.66  E-value=1.4e-16  Score=134.34  Aligned_cols=85  Identities=15%  Similarity=0.257  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+|||.++++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+ +++..|+|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3467899999999999999999999999999999999999999999999999999999999998 899999999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +..+..
T Consensus       149 a~~~~~  154 (165)
T 1rk8_A          149 CFVKGP  154 (165)
T ss_dssp             SEECC-
T ss_pred             ecCCCC
Confidence            876544

>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=99.66  E-value=7.3e-17  Score=127.59  Aligned_cols=86  Identities=26%  Similarity=0.271  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ...+++|||+|||.++|+++|+++|+.||.|.++.+..+..+++++|||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3467999999999999999999999999998433332222278899999999999999999998 899999999999999


Q ss_pred             CCCCCCC
Q psy6490         237 ATPKNRP  243 (398)
Q Consensus       237 ~~~~~~~  243 (398)
                      +..+...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876553

>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=99.66  E-value=2.3e-16  Score=118.39  Aligned_cols=74  Identities=19%  Similarity=0.287  Sum_probs=66.1

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||+++++++|+++|++| .|.++++.      +++|||||+|.+.++|++++ .|||..++|+.|+|+|+.
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            45789999999999999999999999 99999884      56899999999988776666 599999999999999986


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      .+
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.65  E-value=4.5e-17  Score=122.30  Aligned_cols=77  Identities=30%  Similarity=0.611  Sum_probs=66.6

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..++|||+|||.++++++|+++|++||.|.+|+|+++     ++|||||+|++.++|+++... ...++|+.|+|.++.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            4688999999999999999999999999999998765     689999999999888764332 3456999999999988


Q ss_pred             hHH
Q psy6490         328 KEA  330 (398)
Q Consensus       328 k~~  330 (398)
                      +..
T Consensus        78 ~~~   80 (88)
T 1wf0_A           78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

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

Probab=99.65  E-value=1e-16  Score=122.35  Aligned_cols=78  Identities=21%  Similarity=0.344  Sum_probs=67.8

Q ss_pred             CccccceeecCCCC-CCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         246 GNRTKKIFVGGVSQ-DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       246 ~~~~~~l~V~nLp~-~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      ....++|||+|||. ++++++|+++|++||.|.+|++.        +|||||+|++.++|++++ .||+..++|+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34678999999998 99999999999999999999883        789999999988877766 599999999999999


Q ss_pred             ecCchHHH
Q psy6490         324 KAQPKEAV  331 (398)
Q Consensus       324 ~a~~k~~~  331 (398)
                      |+.++...
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99776543

>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=99.65  E-value=2.3e-16  Score=130.83  Aligned_cols=121  Identities=17%  Similarity=0.314  Sum_probs=90.7

Q ss_pred             CCCChhhHhhhhCCC-ccccccceeeeecCCCC--------CCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcC
Q psy6490         115 TGDDPTSAKLFVGGL-NVVREAHQLVLVNGKSS--------GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMF  185 (398)
Q Consensus       115 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~  185 (398)
                      .+.+...+..+...+ ++....+ ...++....        ...............++|||+|||.++|+++|+++|+.|
T Consensus        19 e~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~   97 (150)
T 2i2y_A           19 EAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYY   97 (150)
T ss_dssp             ECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHH
T ss_pred             eecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhh
Confidence            366677776666555 4433333 333332211        111111223344578999999999999999999999999


Q ss_pred             CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCC
Q psy6490         186 GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKN  241 (398)
Q Consensus       186 G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~  241 (398)
                      |.|.+|+++++     ++|||||+|.+.++|.+|++ +++..++|+.|.|.++..+.
T Consensus        98 G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           98 GPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             SCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999887     58999999999999999998 89999999999999987653

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.4e-16  Score=119.07  Aligned_cols=77  Identities=22%  Similarity=0.373  Sum_probs=67.5

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+||  ++|+++|+++|++||.|.+|.|.      .++|||||+|++.++|++++ +||+..|+|+.|+|.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345689999996  99999999999999999999884      45899999999987776666 7999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +.++..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            987653

>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=99.65  E-value=1.2e-16  Score=124.30  Aligned_cols=79  Identities=10%  Similarity=0.219  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C--CCcccCCcccC
Q psy6490         158 DPTSAKLFVGGLSWQ-TSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V--PIHTLDGKKID  233 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~-~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~--~~~~~~g~~l~  233 (398)
                      ..++++|||+|||++ +++++|+++|+.||.|.+|+|++      +||||||+|.+.++|++|++ +  ++..++|+.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            447899999999998 99999999999999999999975      48999999999999999998 4  34569999999


Q ss_pred             CCCCCCCCC
Q psy6490         234 PKHATPKNR  242 (398)
Q Consensus       234 v~~~~~~~~  242 (398)
                      |.++..+..
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999876554

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

Probab=99.65  E-value=1.2e-15  Score=115.91  Aligned_cols=78  Identities=27%  Similarity=0.428  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ..++|||+|||.++++++|+++|+.||.|.+|  +.++.+++   ||||+|.+.++|++|+++++..++|+.|.|.++..
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCc
Confidence            56899999999999999999999999999987  55655654   99999999999999999999999999999998875


Q ss_pred             CCC
Q psy6490         240 KNR  242 (398)
Q Consensus       240 ~~~  242 (398)
                      +..
T Consensus        82 ~~~   84 (94)
T 2e5g_A           82 KEF   84 (94)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            543

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

Probab=99.45  E-value=1.2e-17  Score=132.33  Aligned_cols=85  Identities=20%  Similarity=0.405  Sum_probs=79.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEE--------EEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD--------VLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD  228 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~--------~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~  228 (398)
                      ..+.++|||+|||.++++++|+++|++||.|.+        |+++.++.+++++|||||+|.+.++|++|++ +++..++
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            347799999999999999999999999999999        9999998899999999999999999999998 8999999


Q ss_pred             CcccCCCCCCCCCC
Q psy6490         229 GKKIDPKHATPKNR  242 (398)
Q Consensus       229 g~~l~v~~~~~~~~  242 (398)
                      |+.|.|.++..+..
T Consensus        84 g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 GNPIKVSFATRRAD   97 (116)
Confidence            99999999887654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.64  E-value=8.5e-16  Score=122.38  Aligned_cols=78  Identities=14%  Similarity=0.239  Sum_probs=67.4

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHH-HHCCceeCC--EEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF-GFVTFENEEVVDHIC-EIHFHMIKN--KKVEC  322 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~-afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v  322 (398)
                      ....+|||+||++.+|+++|+++|++||.|.+|+|+.+.     +|| |||+|++.++|++|+ .|||..|.|  +.|+|
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 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            345578999999999999999999999999999887652     677 999999977665554 799999988  99999


Q ss_pred             EecCchH
Q psy6490         323 KKAQPKE  329 (398)
Q Consensus       323 ~~a~~k~  329 (398)
                      .|++++.
T Consensus       101 ~~ak~~~  107 (130)
T 3zzy_A          101 DFSKLTS  107 (130)
T ss_dssp             EECSCSS
T ss_pred             EecCCCc
Confidence            9998764

>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=99.64  E-value=4.1e-16  Score=121.96  Aligned_cols=79  Identities=18%  Similarity=0.473  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|+++++      +|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            36789999999999999999999999999999999886      7899999999999999996 8999999999999999


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus        97 ~~~~~~  102 (109)
T 1x4g_A           97 KESPDM  102 (109)
T ss_dssp             CCCCSS
T ss_pred             CCCCCC
Confidence            876553

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

Probab=99.64  E-value=5.7e-16  Score=136.40  Aligned_cols=102  Identities=19%  Similarity=0.365  Sum_probs=83.1

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++|+++|+++|+.||.|++|+|+++..+++++|||||+|.+.++|+++++ ||+..|+|+.|+|.++.
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            46789999999999999999999999999999999998899999999999999888877775 99999999999999988


Q ss_pred             chHHHhhh-------hhcCCccccCCCCCC
Q psy6490         327 PKEAVQAN-------LLVGKRVILGPLGLR  349 (398)
Q Consensus       327 ~k~~~~~~-------~~~~~~~~~~~~~~~  349 (398)
                      .+......       ....+.++++++...
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~  136 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQD  136 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTT
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCc
Confidence            76543321       133456677665443

>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=99.64  E-value=4e-16  Score=121.46  Aligned_cols=77  Identities=13%  Similarity=0.263  Sum_probs=66.0

Q ss_pred             ccccceee--cCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee-----CCE
Q psy6490         247 NRTKKIFV--GGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI-----KNK  318 (398)
Q Consensus       247 ~~~~~l~V--~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i-----~g~  318 (398)
                      .++++|||  +||++++++++|+++|++||.|++|.|..+      ||||||+|++.++|++|+ +|||+.|     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            45678999  779999999999999999999999887542      799999999977776555 6999998     799


Q ss_pred             EEEEEecCchH
Q psy6490         319 KVECKKAQPKE  329 (398)
Q Consensus       319 ~i~v~~a~~k~  329 (398)
                      .|.|.++....
T Consensus        97 ~l~v~~a~~~p  107 (114)
T 2cq2_A           97 TLYLNFVEKVQ  107 (114)
T ss_dssp             ECEEEEESCCC
T ss_pred             EEEEEecccCc
Confidence            99999987543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=1.9e-15  Score=119.87  Aligned_cols=76  Identities=14%  Similarity=0.184  Sum_probs=64.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHH-HHCCceeCC--EEEEEE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF-GFVTFENEEVVDHIC-EIHFHMIKN--KKVECK  323 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~-afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v~  323 (398)
                      ....|||+||++.+|+++|+++|++||.|++|+|+..      +|| |||+|++.++|.+|+ .|||..|.|  +.|+|.
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            3445789999999999999999999999999998642      376 999999977665555 799999987  699999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      +++++.
T Consensus        98 ~Ak~~~  103 (124)
T 2e5i_A           98 YARPTR  103 (124)
T ss_dssp             CCSCSC
T ss_pred             EecCCc
Confidence            998775

>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=99.64  E-value=6.7e-16  Score=115.49  Aligned_cols=72  Identities=14%  Similarity=0.384  Sum_probs=65.5

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCcee
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQF----G-------KVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMI  315 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~----G-------~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i  315 (398)
                      ...++|||+|||.++++++|+++|+.|    |       .|.++++.++      +|||||+|.+.++|++++.|||..|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCEE
Confidence            457899999999999999999999999    8       8999998755      7999999999888877779999999


Q ss_pred             CCEEEEEEe
Q psy6490         316 KNKKVECKK  324 (398)
Q Consensus       316 ~g~~i~v~~  324 (398)
                      +|+.|+|++
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999975

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.5e-15  Score=116.59  Aligned_cols=77  Identities=29%  Similarity=0.450  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcC--CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMF--GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~--G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ....++|||+|||.++++++|+++|++|  |.|.+|++.        +|||||+|.+.++|++|++ +++..++|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3477999999999999999999999999  999998873        6799999999999999999 9999999999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++..+..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.63  E-value=1.5e-16  Score=124.12  Aligned_cols=77  Identities=14%  Similarity=0.122  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ..++|||+|||+++++++|+++|++|| .|..+++..+    .++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            568999999999999999999999999 8999988643    379999999999999999997 9999999999999887


Q ss_pred             CCC
Q psy6490         238 TPK  240 (398)
Q Consensus       238 ~~~  240 (398)
                      ...
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.63  E-value=1.7e-15  Score=117.09  Aligned_cols=84  Identities=15%  Similarity=0.152  Sum_probs=70.6

Q ss_pred             ccccceeecCCCC-----CCCHHHHHHHHhhcCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHH-HHHHCCceeCCEE
Q psy6490         247 NRTKKIFVGGVSQ-----DTSAEEVKAYFSQFGKVEETVMLMDQQT-KRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKK  319 (398)
Q Consensus       247 ~~~~~l~V~nLp~-----~~tee~L~~~F~~~G~i~~v~i~~~~~~-~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~  319 (398)
                      ..+++|+|+||..     +.++++|+++|++||.|.+|+|++++.+ ++++|||||+|.+.++|.+ +.+|||..++||.
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            4578899999953     2378999999999999999999998654 6899999999999776655 5579999999999


Q ss_pred             EEEEecCchHH
Q psy6490         320 VECKKAQPKEA  330 (398)
Q Consensus       320 i~v~~a~~k~~  330 (398)
                      |+|.++....-
T Consensus        86 i~v~~a~~~~f   96 (105)
T 2pe8_A           86 VKACFYNLDKF   96 (105)
T ss_dssp             CEEEECCHHHH
T ss_pred             EEEEEcCHHHh
Confidence            99999986443

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

Probab=99.63  E-value=4.2e-16  Score=121.55  Aligned_cols=79  Identities=24%  Similarity=0.497  Sum_probs=71.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       156 ~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ..+...++|||+|||.++++++|+++|++||.|.+|++.        +|||||+|.+.++|++|++ +++..++|+.|.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV   97 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            344578999999999999999999999999999999997        7899999999999999998 8999999999999


Q ss_pred             CCCCCCCC
Q psy6490         235 KHATPKNR  242 (398)
Q Consensus       235 ~~~~~~~~  242 (398)
                      .++.....
T Consensus        98 ~~a~~~~~  105 (108)
T 2jvo_A           98 VYSKLPAK  105 (108)
T ss_dssp             ESCSCCC-
T ss_pred             EEecCCCC
Confidence            99876543

>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=6.1e-16  Score=130.45  Aligned_cols=84  Identities=32%  Similarity=0.718  Sum_probs=77.2

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|+++++ ++..++|+.|.|.++.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            46789999999999999999999999999999999999999999999999999998888887 47899999999999988


Q ss_pred             hHHHh
Q psy6490         328 KEAVQ  332 (398)
Q Consensus       328 k~~~~  332 (398)
                      +....
T Consensus        81 ~~~~~   85 (167)
T 2cjk_A           81 RDEQD   85 (167)
T ss_dssp             HHHHH
T ss_pred             hhhcc
Confidence            76543

>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=99.63  E-value=6.5e-16  Score=119.53  Aligned_cols=77  Identities=26%  Similarity=0.455  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++|+++|+++|++||.|.+|+++        ++||||+|.+.++|++|++ +++..|+|+.|.|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            367999999999999999999999999999999986        4599999999999999998 8999999999999998


Q ss_pred             CCCCCC
Q psy6490         238 TPKNRP  243 (398)
Q Consensus       238 ~~~~~~  243 (398)
                      ..+...
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            776543

>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=99.63  E-value=6.9e-16  Score=117.92  Aligned_cols=76  Identities=26%  Similarity=0.494  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         157 DDPTSAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ....+++|||+|||. ++++++|+++|+.||.|.++++        ++|||||+|.+.++|.+|++ +++..++|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE--------CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344789999999998 9999999999999999999998        37899999999999999998 8999999999999


Q ss_pred             CCCCCC
Q psy6490         235 KHATPK  240 (398)
Q Consensus       235 ~~~~~~  240 (398)
                      .++..+
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            988754

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

Probab=99.62  E-value=8.8e-16  Score=130.64  Aligned_cols=83  Identities=27%  Similarity=0.379  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|++|.|..++ ++.++|||||+|.+.++|++|++ +++..|+|+.|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34467999999999999999999999999999999999998 89999999999999999999998 99999999999998


Q ss_pred             CCCCC
Q psy6490         236 HATPK  240 (398)
Q Consensus       236 ~~~~~  240 (398)
                      ++...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            87653

>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=99.62  E-value=2.3e-16  Score=120.69  Aligned_cols=81  Identities=19%  Similarity=0.408  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLR----EYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~----~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .++++|||+|||.++++++|+    ++|++||.|.+|++.+   ++.++|||||+|.+.++|.+|++ +++..++|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            377999999999999999999    9999999999999874   56789999999999999999998 899999999999


Q ss_pred             CCCCCCCCC
Q psy6490         234 PKHATPKNR  242 (398)
Q Consensus       234 v~~~~~~~~  242 (398)
                      |.++..+..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999876543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=3.3e-16  Score=119.53  Aligned_cols=81  Identities=21%  Similarity=0.304  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|++ +++..++|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34478999999999999999999999999988766     2367899999999999999999999 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++..+..
T Consensus        87 ~a~~~~~   93 (96)
T 1fjc_A           87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EcCCCCC
Confidence            9876543

>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=99.62  E-value=5.2e-16  Score=116.53  Aligned_cols=78  Identities=29%  Similarity=0.526  Sum_probs=63.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      .....+|||+|||+++|+++|+++|++||.|.+|+++++     +||||||+|.+.++|+++... ...++|+.|.|.++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~~-~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE-DLIIKGISVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTTC-EEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcCC-CcccCCEEEEEEEc
Confidence            347899999999999999999999999999999999886     699999999999999964332 44467999999888


Q ss_pred             CCCC
Q psy6490         238 TPKN  241 (398)
Q Consensus       238 ~~~~  241 (398)
                      .++.
T Consensus        82 ~~k~   85 (89)
T 3d2w_A           82 EPKH   85 (89)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            7654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=115.47  Aligned_cols=78  Identities=24%  Similarity=0.459  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+|||.++++++|+++|++||.|.+|++++        +||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            34789999999999999999999999999999999963        499999999999999997 899999999999999


Q ss_pred             CCCCCCC
Q psy6490         237 ATPKNRP  243 (398)
Q Consensus       237 ~~~~~~~  243 (398)
                      +..+...
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9876543

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

Probab=99.61  E-value=9.7e-16  Score=120.82  Aligned_cols=78  Identities=23%  Similarity=0.456  Sum_probs=66.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHH-HCCceeCCEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT---KRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVEC  322 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~---~~~kg~afV~F~~~eaa~a~~~-l~~~~i~g~~i~v  322 (398)
                      ...++|||+|||+++|+++|+++|++||.|. +.++.+..+   |+++|||||+|++.++|++|++ |  ..++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~--~~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC--LEEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS--EEETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh--hhcCCcEEEe
Confidence            3568899999999999999999999999999 888888777   7999999999999888877664 5  3477777777


Q ss_pred             EecCc
Q psy6490         323 KKAQP  327 (398)
Q Consensus       323 ~~a~~  327 (398)
                      ..+..
T Consensus        83 ~~~~~   87 (114)
T 2dnl_A           83 VSSPT   87 (114)
T ss_dssp             ECCSS
T ss_pred             ccCCC
Confidence            66544

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.7e-15  Score=113.89  Aligned_cols=78  Identities=18%  Similarity=0.310  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+||  ++|+++|+++|++||.|.+|++.      .++|||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            346799999996  99999999999999999999984      368999999999999999996 899999999999999


Q ss_pred             CCCCCCC
Q psy6490         237 ATPKNRP  243 (398)
Q Consensus       237 ~~~~~~~  243 (398)
                      +..+...
T Consensus        84 a~~~~~~   90 (97)
T 1x5p_A           84 ARKQPML   90 (97)
T ss_dssp             CSSCCCC
T ss_pred             CCCCCCC
Confidence            9776543

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

Probab=99.61  E-value=1.1e-15  Score=116.60  Aligned_cols=79  Identities=14%  Similarity=0.144  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEE-EEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDV-LIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~-~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+| .++.++.++    .|||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            357899999999999999999999999999999 488876443    49999999999999998 899999999999999


Q ss_pred             CCCCC
Q psy6490         237 ATPKN  241 (398)
Q Consensus       237 ~~~~~  241 (398)
                      +.++.
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            88763

>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=99.61  E-value=2.1e-15  Score=124.70  Aligned_cols=79  Identities=11%  Similarity=0.244  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC--cccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG--KKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g--~~l~v~~  236 (398)
                      ...+|||+||++++|+++|+++|++||+|++|++..++    ++|||||+|.+.++|++|++ +++..|.|  ++|+|.+
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            56789999999999999999999999999999997553    58899999999999999998 99999965  9999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      ++.+..
T Consensus       121 Ak~~~l  126 (164)
T 1sjr_A          121 SKLTSL  126 (164)
T ss_dssp             CSSSSC
T ss_pred             ecCCcc
Confidence            887643

>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=99.61  E-value=2e-15  Score=118.21  Aligned_cols=76  Identities=16%  Similarity=0.397  Sum_probs=69.5

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         159 PTSAKLFVGGLSWQ-TSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp~~-~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ...++|||+|||.+ +++++|+++|++||.|.+|++        ++|||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            35689999999999 999999999999999999998        48899999999999999996 899999999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +.....
T Consensus        97 a~~~~~  102 (110)
T 1wf1_A           97 AGEPKP  102 (110)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            875443

>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=99.61  E-value=7e-16  Score=121.80  Aligned_cols=75  Identities=19%  Similarity=0.322  Sum_probs=63.3

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEE-----EE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKK-----VE  321 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~-----i~  321 (398)
                      ..++|||+|||+++++++|+++|++||.|++|.|+.+       |||||+|++.++|++|+ .||+..|+|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4678999999999999999999999999999999766       89999999987776666 59999999998     77


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |..+.++.
T Consensus        88 v~~~~~~~   95 (115)
T 3beg_B           88 VKVDGPRS   95 (115)
T ss_dssp             EEECC---
T ss_pred             eccCCCCC
Confidence            77776644

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

Probab=99.61  E-value=9.5e-16  Score=116.98  Aligned_cols=76  Identities=29%  Similarity=0.545  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         159 PTSAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      .+.++|||+|||. ++++++|+++|++||.|.+|++.        +|||||+|.+.++|++|++ +++..+.|+.|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4789999999998 99999999999999999999983        7899999999999999998 899999999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +..+..
T Consensus        80 a~~~~~   85 (96)
T 2kvi_A           80 SSSNAR   85 (96)
T ss_dssp             EECCCC
T ss_pred             cCcCCC
Confidence            876554

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

Probab=99.61  E-value=1.4e-15  Score=114.57  Aligned_cols=77  Identities=22%  Similarity=0.410  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+|||.++|+++|+++|++||.|.+|++++        +||||+|.+.++|++|++ +++..++|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34789999999999999999999999999999999974        499999999999999998 899999999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +.....
T Consensus        78 a~~~~~   83 (90)
T 2dnp_A           78 STKGQK   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            887644

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.61  E-value=5.8e-16  Score=120.95  Aligned_cols=78  Identities=13%  Similarity=0.175  Sum_probs=69.5

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcC----hHh----HHHHHh---CCCcc
Q psy6490         162 AKLFVGGL----SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE----PET----VEKVLK---VPIHT  226 (398)
Q Consensus       162 ~~l~v~nL----p~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~----~e~----a~~al~---~~~~~  226 (398)
                      ..|||+||    ++++++++|+++|+.||+|.+|+++.|+.||+++|||||+|.+    +++    |.+|++   +++..
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    433    788876   59999


Q ss_pred             cCCcccCCCCCCC
Q psy6490         227 LDGKKIDPKHATP  239 (398)
Q Consensus       227 ~~g~~l~v~~~~~  239 (398)
                      ++|++|+|.....
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            9999999986553

>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=99.60  E-value=5.1e-16  Score=121.74  Aligned_cols=75  Identities=17%  Similarity=0.267  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|++||.|.+|++.+      ++|||||+|.+.++|++|++ +++..++|+.|.|.++.
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            568999999999999999999999999999999875      48899999999999999998 89999999999999876


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.4e-15  Score=112.29  Aligned_cols=72  Identities=10%  Similarity=0.173  Sum_probs=61.7

Q ss_pred             ccc-eeecCCCCCCCHHH----HHHHHhhc-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         249 TKK-IFVGGVSQDTSAEE----VKAYFSQF-GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       249 ~~~-l~V~nLp~~~tee~----L~~~F~~~-G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      +.+ |||+|||+++++++    |+++|++| |.|.+|       ++   |+|||+|.+.++|.+|+ +|+|..|.||.|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            444 99999999999988    55899999 599987       33   99999999988776655 7999999999999


Q ss_pred             EEecCchHH
Q psy6490         322 CKKAQPKEA  330 (398)
Q Consensus       322 v~~a~~k~~  330 (398)
                      |.+|+.+.+
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999987654

>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=99.59  E-value=9.6e-16  Score=116.22  Aligned_cols=77  Identities=19%  Similarity=0.413  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCC-EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCC-cccCCcccCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPI-HTLDGKKIDPK  235 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~-i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~-~~~~g~~l~v~  235 (398)
                      ...++|||+|||.++|+++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++ +++ ..++|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            36789999999999999999999999999 6666552       48899999999999999998 898 89999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++..+..
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9887654

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

Probab=99.59  E-value=2.1e-15  Score=118.84  Aligned_cols=76  Identities=25%  Similarity=0.384  Sum_probs=65.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCC---CCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT---QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~---~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      ..++|||+|||.++|+++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++||+.. ..++|+.|.+..
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~-~~~~G~~~~~~~   84 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC-LEEDGKLYLCVS   84 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS-EEETTEEEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh-hhcCCcEEEecc
Confidence            679999999999999999999999999999 888888777   799999999999999999999832 246777776654


Q ss_pred             C
Q psy6490         237 A  237 (398)
Q Consensus       237 ~  237 (398)
                      .
T Consensus        85 ~   85 (114)
T 2dnl_A           85 S   85 (114)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.58  E-value=2e-15  Score=112.86  Aligned_cols=71  Identities=20%  Similarity=0.492  Sum_probs=66.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcC----C-------CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMF----G-------AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD  228 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~----G-------~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~  228 (398)
                      ..++|||+|||.++++++|+++|++|    |       .|.++++.++      +|||||+|.+.++|++|+.+++..++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCEEC
Confidence            67999999999999999999999999    8       9999999765      89999999999999999999999999


Q ss_pred             CcccCCCC
Q psy6490         229 GKKIDPKH  236 (398)
Q Consensus       229 g~~l~v~~  236 (398)
                      |+.|.|++
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99998764

>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=99.58  E-value=1.4e-15  Score=114.08  Aligned_cols=78  Identities=31%  Similarity=0.539  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      .+++|||+|||.++++++|+++|++||.|.+|+++++     ++|||||+|.+.++|++++.. ...++|+.|.|.++.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            6799999999999999999999999999999999876     699999999999999876554 4567999999999887


Q ss_pred             CCCC
Q psy6490         240 KNRP  243 (398)
Q Consensus       240 ~~~~  243 (398)
                      +...
T Consensus        78 ~~~~   81 (88)
T 1wf0_A           78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6553

>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=99.58  E-value=3.9e-15  Score=129.87  Aligned_cols=76  Identities=16%  Similarity=0.302  Sum_probs=68.2

Q ss_pred             cccceeecCCC-CCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         248 RTKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       248 ~~~~l~V~nLp-~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      .+++|||+||+ +++|+++|+++|+.||.|.+|+|++++     +|||||+|++.++|++|+ .|||..|.|+.|+|.|+
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 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46789999999 899999999999999999999998763     799999999987776665 69999999999999998


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      +.+
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=7.9e-15  Score=108.28  Aligned_cols=73  Identities=18%  Similarity=0.241  Sum_probs=64.8

Q ss_pred             CCcE-EEEcCCCCCCCHHH----HHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         160 TSAK-LFVGGLSWQTSSEK----LREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       160 ~~~~-l~v~nLp~~~t~~~----L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      ++.+ |||+|||+++++++    |+++|++|| +|.+|       ++   |+|||+|.+.++|.+|++ +++..+.||.|
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            3455 99999999999988    558999994 99998       33   999999999999999998 99999999999


Q ss_pred             CCCCCCCCCC
Q psy6490         233 DPKHATPKNR  242 (398)
Q Consensus       233 ~v~~~~~~~~  242 (398)
                      +|.++..+..
T Consensus        77 ~v~~A~~~sd   86 (96)
T 2diu_A           77 IVSFTPKNRE   86 (96)
T ss_dssp             EEESSCCSCC
T ss_pred             EEEecCCCcc
Confidence            9999987655

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

Probab=99.57  E-value=6e-15  Score=130.24  Aligned_cols=106  Identities=14%  Similarity=0.260  Sum_probs=76.5

Q ss_pred             HhCCCcccCCcccCCCCCCCCC-CCccCccccceeecCCCCCC---------CHHHHHHHHhhcCCeeEEEEeecCCCCC
Q psy6490         220 LKVPIHTLDGKKIDPKHATPKN-RPKIGNRTKKIFVGGVSQDT---------SAEEVKAYFSQFGKVEETVMLMDQQTKR  289 (398)
Q Consensus       220 l~~~~~~~~g~~l~v~~~~~~~-~~~~~~~~~~l~V~nLp~~~---------tee~L~~~F~~~G~i~~v~i~~~~~~~~  289 (398)
                      +..+...+.|+.....+..... ........++|||+||+.++         +|++|+++|++||.|++|+|+.+     
T Consensus       104 ~~~~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----  178 (240)
T 3u1l_A          104 LRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----  178 (240)
T ss_dssp             HHCSSBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----
T ss_pred             ccccCcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----
Confidence            3334444556655444333221 12234567899999999998         79999999999999999999864     


Q ss_pred             cceEEEEEeCCHHHHHHHH-HHCCcee------------CCEEEEEEecCchHHH
Q psy6490         290 HRGFGFVTFENEEVVDHIC-EIHFHMI------------KNKKVECKKAQPKEAV  331 (398)
Q Consensus       290 ~kg~afV~F~~~eaa~a~~-~l~~~~i------------~g~~i~v~~a~~k~~~  331 (398)
                       ||||||+|.+.++|+.|+ .|+|..|            .|+.|.|+||+.+...
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             899999999988877666 6999999            8999999999876543

>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=99.57  E-value=1.7e-15  Score=113.52  Aligned_cols=75  Identities=12%  Similarity=0.259  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|++| .|.++++.      +++|||||+|.+.++|++|++ +++..++|++|.|.++.
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            56899999999999999999999999 99999884      479999999999999999998 89999999999999886


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>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=99.57  E-value=2.1e-15  Score=117.35  Aligned_cols=73  Identities=16%  Similarity=0.265  Sum_probs=63.4

Q ss_pred             CCcEEEE--cCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc-----CCcc
Q psy6490         160 TSAKLFV--GGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL-----DGKK  231 (398)
Q Consensus       160 ~~~~l~v--~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~-----~g~~  231 (398)
                      ++++|||  +||+.++++++|+++|++||.|.+|.+..      .||||||+|.+.++|++|++ +++..+     .|+.
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            6789999  77999999999999999999999998864      38999999999999999998 888876     5666


Q ss_pred             cCCCCCC
Q psy6490         232 IDPKHAT  238 (398)
Q Consensus       232 l~v~~~~  238 (398)
                      |.|.++.
T Consensus        98 l~v~~a~  104 (114)
T 2cq2_A           98 LYLNFVE  104 (114)
T ss_dssp             CEEEEES
T ss_pred             EEEEecc
Confidence            7665554

>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=99.57  E-value=2e-15  Score=128.33  Aligned_cols=121  Identities=16%  Similarity=0.190  Sum_probs=101.0

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      ..++++..+.+...+..++ .+++....+....+.......      .......++|||+|||.++++++|+++|+.||.
T Consensus        53 ~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~~~~------~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~  125 (175)
T 1fje_B           53 NRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRD------SKKVRAARTLLAKNLSFNITEDELKEVFEDALE  125 (175)
T ss_dssp             TTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCCCSS------CSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSE
T ss_pred             cccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCCCcc------ccccccCCEEEEeCCCCCCCHHHHHHHHHhcCe
Confidence            4578889999999999999 488777777766665544322      123347799999999999999999999999998


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      |..+     ..++.++|||||+|.+.++|.+|++ +++..++|+.|.|.++.++
T Consensus       126 v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          126 IRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             EEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            8766     4578899999999999999999999 8999999999999988754

>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=99.57  E-value=5.5e-15  Score=125.45  Aligned_cols=98  Identities=22%  Similarity=0.403  Sum_probs=80.0

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHH-HHCCceeC---CEEEE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTK--RHRGFGFVTFENEEVVDHIC-EIHFHMIK---NKKVE  321 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~--~~kg~afV~F~~~eaa~a~~-~l~~~~i~---g~~i~  321 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+|+++++..++  +++|||||+|.+.++|++++ .||+..+.   ++.+.
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            46789999999999999999999999999999999998876  89999999999988887766 59998876   68888


Q ss_pred             EEecCchHHHhhhhhcCCccccCCCCC
Q psy6490         322 CKKAQPKEAVQANLLVGKRVILGPLGL  348 (398)
Q Consensus       322 v~~a~~k~~~~~~~~~~~~~~~~~~~~  348 (398)
                      +.++..+....   ...+.++++++..
T Consensus        82 ~~~~~~~~~~~---~~~~~l~v~nl~~  105 (175)
T 3nmr_A           82 MKPADSEKNNA---VEDRKLFIGMISK  105 (175)
T ss_dssp             EEECGGGCCSC---GGGSEEEEESCCT
T ss_pred             Ecccccccccc---CCCCeEEEcCCCC
Confidence            88876554321   2345566666543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=2.6e-14  Score=113.28  Aligned_cols=76  Identities=14%  Similarity=0.186  Sum_probs=66.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccE-EEEEEcChHhHHHHHh-CCCcccCC--cccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF-GFITFAEPETVEKVLK-VPIHTLDG--KKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~-afV~f~~~e~a~~al~-~~~~~~~g--~~l~v~  235 (398)
                      ....|||+||++.+|+++|+++|++||.|.+|++...      .|| |||+|.+.++|.+|++ +++..|.|  +.|+|.
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            3455789999999999999999999999999999753      376 9999999999999998 89999987  589998


Q ss_pred             CCCCCC
Q psy6490         236 HATPKN  241 (398)
Q Consensus       236 ~~~~~~  241 (398)
                      ++..+.
T Consensus        98 ~Ak~~~  103 (124)
T 2e5i_A           98 YARPTR  103 (124)
T ss_dssp             CCSCSC
T ss_pred             EecCCc
Confidence            887664

>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=99.56  E-value=3.7e-15  Score=117.63  Aligned_cols=71  Identities=17%  Similarity=0.273  Sum_probs=63.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ..++|||+|||.++++++|+++|++||.|.+|+|+.+       |||||+|.+.++|++||+ +++..|+|+.|.+.+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            5689999999999999999999999999999999765       899999999999999999 8999999999655443

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=6.5e-15  Score=117.29  Aligned_cols=78  Identities=13%  Similarity=0.305  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccE-EEEEEcChHhHHHHHh-CCCcccCC--cccCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF-GFITFAEPETVEKVLK-VPIHTLDG--KKIDPK  235 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~-afV~f~~~e~a~~al~-~~~~~~~g--~~l~v~  235 (398)
                      .-..|||+||++.+|+++|+++|++||.|.+|++..+     .+|| |||+|.+.++|++|++ +++..|.|  +.|+|.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            5578889999999999999999999999999998875     3688 9999999999999998 89999988  889999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      +++....
T Consensus       102 ~ak~~~l  108 (130)
T 3zzy_A          102 FSKLTSL  108 (130)
T ss_dssp             ECSCSSC
T ss_pred             ecCCCce
Confidence            9876643

>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=99.56  E-value=5.4e-16  Score=127.53  Aligned_cols=81  Identities=21%  Similarity=0.311  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEE--------EEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDV--------LIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG  229 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~--------~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g  229 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.++        ++.   .+++++|||||+|.+.++|.+|++ +++..++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            367999999999999999999999999988764        332   368899999999999999999999 89999999


Q ss_pred             cccCCCCCCCCCC
Q psy6490         230 KKIDPKHATPKNR  242 (398)
Q Consensus       230 ~~l~v~~~~~~~~  242 (398)
                      +.|.|.++.....
T Consensus       120 ~~l~V~~a~~~~~  132 (143)
T 3egn_A          120 KPMVVQFARSARP  132 (143)
T ss_dssp             EECEEEECCCSCC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999876543

>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=99.55  E-value=1.6e-14  Score=113.45  Aligned_cols=82  Identities=12%  Similarity=0.265  Sum_probs=67.7

Q ss_pred             cCccccceeecCCCCCCC-----------HHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCC
Q psy6490         245 IGNRTKKIFVGGVSQDTS-----------AEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHF  312 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~t-----------ee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~  312 (398)
                      ....+++|+|+||....+           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|++|+ .|||
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            445688999999944432           6899999999999999965 553   37999999999987776655 7999


Q ss_pred             ceeCCEEEEEEecCchHH
Q psy6490         313 HMIKNKKVECKKAQPKEA  330 (398)
Q Consensus       313 ~~i~g~~i~v~~a~~k~~  330 (398)
                      ..|+||.|+|.|+.++..
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999987654

>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=99.55  E-value=9.2e-15  Score=126.15  Aligned_cols=80  Identities=13%  Similarity=0.264  Sum_probs=73.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++.++. ++.++|||||+|.+.++|++|++..+..++|+.|.|.+...
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            46899999999999999999999999999999999987 58899999999999999999999767799999999987765


Q ss_pred             C
Q psy6490         240 K  240 (398)
Q Consensus       240 ~  240 (398)
                      .
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.55  E-value=1.4e-14  Score=133.00  Aligned_cols=82  Identities=20%  Similarity=0.360  Sum_probs=72.9

Q ss_pred             CccccceeecCCCCCCCHHHHH----HHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKV  320 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~----~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i  320 (398)
                      ....++|||+|||+++|+++|+    ++|+.||.|++|++++   +++++|||||+|.+.++|++++ .|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4567899999999999999977    8999999999998875   6788999999999988777766 799999999999


Q ss_pred             EEEecCchHH
Q psy6490         321 ECKKAQPKEA  330 (398)
Q Consensus       321 ~v~~a~~k~~  330 (398)
                      +|.|++.+..
T Consensus        83 ~v~~a~~~~~   92 (282)
T 3pgw_A           83 RIQYAKTDSD   92 (282)
T ss_pred             EEEEeccCcc
Confidence            9999977553

>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=99.54  E-value=9.3e-15  Score=141.66  Aligned_cols=82  Identities=20%  Similarity=0.447  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++|+++|+++|+.||.|+.|.|+.++.++.++|||||+|.+.++|.+||+ +++..|+|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            367899999999999999999999999999999999999999999999999999999999996 8999999999999988


Q ss_pred             CCC
Q psy6490         238 TPK  240 (398)
Q Consensus       238 ~~~  240 (398)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            754

>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=99.53  E-value=2.8e-14  Score=110.31  Aligned_cols=83  Identities=17%  Similarity=0.147  Sum_probs=69.1

Q ss_pred             cccceeecCC--CCCCC--------HHHHHHHHhhcCCeeEEEEeecCCC--CCcceEEEEEeCCHHHHHHH-HHHCCce
Q psy6490         248 RTKKIFVGGV--SQDTS--------AEEVKAYFSQFGKVEETVMLMDQQT--KRHRGFGFVTFENEEVVDHI-CEIHFHM  314 (398)
Q Consensus       248 ~~~~l~V~nL--p~~~t--------ee~L~~~F~~~G~i~~v~i~~~~~~--~~~kg~afV~F~~~eaa~a~-~~l~~~~  314 (398)
                      ++++|.|.|+  +.++.        ++||++.|++||.|++|+|.++..+  +.++|||||+|++.++|.+| .+|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5678999998  43443        4799999999999999999988755  36899999999997766555 5899999


Q ss_pred             eCCEEEEEEecCchHH
Q psy6490         315 IKNKKVECKKAQPKEA  330 (398)
Q Consensus       315 i~g~~i~v~~a~~k~~  330 (398)
                      ++||.|+|.++....-
T Consensus        84 f~GR~i~v~~~~~~~f   99 (105)
T 3v4m_A           84 FANRVVVTKYCDPDSY   99 (105)
T ss_dssp             ETTEECEEEEECHHHH
T ss_pred             eCCCEEEEEEeCHHHH
Confidence            9999999999876543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=2.4e-14  Score=110.58  Aligned_cols=80  Identities=13%  Similarity=0.150  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCC-----CCCHHHHHHHHhcCCCEEEEEEeeCCCC-CCcccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         160 TSAKLFVGGLSW-----QTSSEKLREYFGMFGAVTDVLIMKDPIT-QRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       160 ~~~~l~v~nLp~-----~~t~~~L~~~f~~~G~i~~~~~~~~~~~-~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      .+++|+|+||-.     +-++++|+++|++||.|.+|+|.+++.+ ++++||+||+|.+.++|.+|++ +++..++||.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            679999999963     2378999999999999999999998654 6899999999999999999998 99999999999


Q ss_pred             CCCCCCC
Q psy6490         233 DPKHATP  239 (398)
Q Consensus       233 ~v~~~~~  239 (398)
                      .+.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9988753

>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=99.52  E-value=6.2e-14  Score=127.23  Aligned_cols=77  Identities=25%  Similarity=0.500  Sum_probs=69.1

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|++.++      +|||||+|.+.++|.+++ .+||..|+|+.|+|.
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEee
Confidence            3456788999999999999999999999999999998654      799999999988887776 599999999999999


Q ss_pred             ecCc
Q psy6490         324 KAQP  327 (398)
Q Consensus       324 ~a~~  327 (398)
                      |+.+
T Consensus        92 ~a~~   95 (261)
T 3sde_A           92 FATH   95 (261)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            9875

>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=99.50  E-value=5.5e-14  Score=110.78  Aligned_cols=82  Identities=16%  Similarity=0.201  Sum_probs=68.4

Q ss_pred             cccceeecCCC--CCC---CHHHHHHHHhhcCCeeEEEEeecCC----CCCcceEEEEEeCCHHHHHH-HHHHCCceeCC
Q psy6490         248 RTKKIFVGGVS--QDT---SAEEVKAYFSQFGKVEETVMLMDQQ----TKRHRGFGFVTFENEEVVDH-ICEIHFHMIKN  317 (398)
Q Consensus       248 ~~~~l~V~nLp--~~~---tee~L~~~F~~~G~i~~v~i~~~~~----~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g  317 (398)
                      ++++|+|+|+-  .++   .++||++.|++||.|.+|+|+++..    +++++||+||+|.+.++|.+ +..|||..++|
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            57889999983  222   3689999999999999999999864    45788999999999776655 55799999999


Q ss_pred             EEEEEEecCchH
Q psy6490         318 KKVECKKAQPKE  329 (398)
Q Consensus       318 ~~i~v~~a~~k~  329 (398)
                      |.|+|.++....
T Consensus        99 R~i~v~~~~~~~  110 (118)
T 3ue2_A           99 RKVVAEVYDQER  110 (118)
T ss_dssp             EECEEEEECHHH
T ss_pred             cEEEEEEcChHh
Confidence            999999987643

>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=99.49  E-value=5.5e-14  Score=124.97  Aligned_cols=126  Identities=17%  Similarity=0.169  Sum_probs=96.9

Q ss_pred             CCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCC---------------------------CCCCCCCC
Q psy6490         109 SGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRST---------------------------PTGDDPTS  161 (398)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~  161 (398)
                      .+++|+.+.+...+..++..+++....+..+.+............                           ......++
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            467889999999999888766665555554444433211100000                           00112357


Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC-CcccCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD-GKKIDPKHAT  238 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~-g~~l~v~~~~  238 (398)
                      ++|||+|||.++++++|+++|+.|| .|.+++++.+     ++|||||+|.+.++|.+|++ +++..++ |+.|.|.++.
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            9999999999999999999999999 9999999764     38899999999999999998 8999999 9999999886


Q ss_pred             C
Q psy6490         239 P  239 (398)
Q Consensus       239 ~  239 (398)
                      +
T Consensus       227 ~  227 (229)
T 2adc_A          227 S  227 (229)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.49  E-value=3.7e-14  Score=123.06  Aligned_cols=126  Identities=17%  Similarity=0.195  Sum_probs=94.7

Q ss_pred             CCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCC---------------------------CCCCCCCCCCCC
Q psy6490         109 SGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDS---------------------------GRSTPTGDDPTS  161 (398)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~~~~  161 (398)
                      .++++..+.+...+..++..+++....+....+........                           ..........++
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            45788888898888888776665444444333332211100                           000001112458


Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC-CEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC-CcccCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD-GKKIDPKHAT  238 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G-~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~-g~~l~v~~~~  238 (398)
                      ++|||+|||.++++++|+++|+.|| .|.+++++.+     .+|||||+|.+.++|.+|++ +++..++ |+.|.|.++.
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            9999999999999999999999999 9999999775     38999999999999999998 8999999 9999998876


Q ss_pred             C
Q psy6490         239 P  239 (398)
Q Consensus       239 ~  239 (398)
                      +
T Consensus       196 ~  196 (198)
T 1qm9_A          196 S  196 (198)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.48  E-value=2.2e-14  Score=110.78  Aligned_cols=71  Identities=17%  Similarity=0.321  Sum_probs=58.7

Q ss_pred             ecCCCCCCCHHHHHHHH------------hhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEE
Q psy6490         254 VGGVSQDTSAEEVKAYF------------SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKV  320 (398)
Q Consensus       254 V~nLp~~~tee~L~~~F------------~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i  320 (398)
                      +.||+..+++++|+++|            ++||.|.+|+|.++. +++++|||||+|++.++|.+|+ .|||+.++||.|
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            44566666777666555            999999999999885 4789999999999977776555 799999999999


Q ss_pred             EEEec
Q psy6490         321 ECKKA  325 (398)
Q Consensus       321 ~v~~a  325 (398)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

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

Probab=99.45  E-value=6.2e-14  Score=123.75  Aligned_cols=79  Identities=20%  Similarity=0.367  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCC---------CHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         158 DPTSAKLFVGGLSWQT---------SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~---------t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      +...++|||+||+.++         +|++|+++|++||.|++|+|+.+      +|||||+|.+.++|+.|++ |++..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4578999999999998         79999999999999999999864      8999999999999999998 889888


Q ss_pred             ------------CCcccCCCCCCCCCC
Q psy6490         228 ------------DGKKIDPKHATPKNR  242 (398)
Q Consensus       228 ------------~g~~l~v~~~~~~~~  242 (398)
                                  .|+.|.|+|+.....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999976543

>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=99.45  E-value=2.7e-13  Score=106.36  Aligned_cols=82  Identities=16%  Similarity=0.291  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEcCCCCCCC-----------HHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCC
Q psy6490         157 DDPTSAKLFVGGLSWQTS-----------SEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPI  224 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t-----------~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~  224 (398)
                      ....+++|+|+||-...+           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|.+|++ +++
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            344789999999944332           5899999999999999966 554   279999999999999999997 999


Q ss_pred             cccCCcccCCCCCCCCCC
Q psy6490         225 HTLDGKKIDPKHATPKNR  242 (398)
Q Consensus       225 ~~~~g~~l~v~~~~~~~~  242 (398)
                      ..++|+.|.|.++..+..
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999876554

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=1e-12  Score=100.18  Aligned_cols=65  Identities=11%  Similarity=0.151  Sum_probs=56.3

Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCchH
Q psy6490         259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       259 ~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      .++++++|+++|++||.|++|+|+     ++++|||||+|++.++|+.|++. +..+.|+.|+|+|++.+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-EVGLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-CCBCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-cCCCCCCeEEEEEccCCC
Confidence            578999999999999999999987     36799999999998888777764 455789999999998764

>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=99.37  E-value=3.9e-13  Score=103.83  Aligned_cols=79  Identities=14%  Similarity=0.160  Sum_probs=69.1

Q ss_pred             CCcEEEEcCC--CCCCC--------HHHHHHHHhcCCCEEEEEEeeCCCC--CCcccEEEEEEcChHhHHHHHh-CCCcc
Q psy6490         160 TSAKLFVGGL--SWQTS--------SEKLREYFGMFGAVTDVLIMKDPIT--QRSRGFGFITFAEPETVEKVLK-VPIHT  226 (398)
Q Consensus       160 ~~~~l~v~nL--p~~~t--------~~~L~~~f~~~G~i~~~~~~~~~~~--~~~~g~afV~f~~~e~a~~al~-~~~~~  226 (398)
                      +++.|.|.|+  +.++.        +++|++.|++||.|.+|+|.+++.+  +.++||+||+|.+.++|.+|++ +|+..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            6899999998  44443        3689999999999999999988754  4689999999999999999998 99999


Q ss_pred             cCCcccCCCCCC
Q psy6490         227 LDGKKIDPKHAT  238 (398)
Q Consensus       227 ~~g~~l~v~~~~  238 (398)
                      ++||.|.+.+..
T Consensus        84 f~GR~i~v~~~~   95 (105)
T 3v4m_A           84 FANRVVVTKYCD   95 (105)
T ss_dssp             ETTEECEEEEEC
T ss_pred             eCCCEEEEEEeC
Confidence            999999887754

>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=99.37  E-value=1.8e-12  Score=101.31  Aligned_cols=81  Identities=10%  Similarity=0.034  Sum_probs=64.7

Q ss_pred             cccceeecCCCC--CC--------CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HHHCCceeC
Q psy6490         248 RTKKIFVGGVSQ--DT--------SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMIK  316 (398)
Q Consensus       248 ~~~~l~V~nLp~--~~--------tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~l~~~~i~  316 (398)
                      .+++|.|+|+=.  +.        .++||++.|++||.|++|.|.++.    ++||+||+|++.++|.+| .+|||..++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            467788888832  21        246899999999999999986652    489999999997766555 579999999


Q ss_pred             CEEEEEEecCchHHHh
Q psy6490         317 NKKVECKKAQPKEAVQ  332 (398)
Q Consensus       317 g~~i~v~~a~~k~~~~  332 (398)
                      ||.|+|.|+....-..
T Consensus        82 GR~i~v~~~~~~~y~~   97 (114)
T 3s6e_A           82 GKMITAAYVPLPTYHN   97 (114)
T ss_dssp             TEECEEEEECHHHHHH
T ss_pred             CEEEEEEEEcHHHHHH
Confidence            9999999997665443

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=8.9e-12  Score=94.93  Aligned_cols=76  Identities=14%  Similarity=0.162  Sum_probs=63.0

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccC
Q psy6490         161 SAKLFVGGLS-------WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID  233 (398)
Q Consensus       161 ~~~l~v~nLp-------~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~  233 (398)
                      .++|.|.-..       .++++++|+++|++||.|.+|+|+.     +++|||||+|.+.++|++|++. ...+.|+.|.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQN-EVGLVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHT-CCBCSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHh-cCCCCCCeEE
Confidence            4566666544       4689999999999999999999983     4799999999999999999985 3447799999


Q ss_pred             CCCCCCCCC
Q psy6490         234 PKHATPKNR  242 (398)
Q Consensus       234 v~~~~~~~~  242 (398)
                      |.++..+..
T Consensus        84 V~~a~~~~~   92 (100)
T 2d9o_A           84 ISWLEGQPQ   92 (100)
T ss_dssp             EECSSCCCC
T ss_pred             EEEccCCCC
Confidence            999876543

>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=99.34  E-value=2.7e-13  Score=104.59  Aligned_cols=71  Identities=18%  Similarity=0.330  Sum_probs=62.3

Q ss_pred             EcCCCCCCCHHHHHHHH------------hcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         166 VGGLSWQTSSEKLREYF------------GMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       166 v~nLp~~~t~~~L~~~f------------~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      +.||+.++++++|++.|            ++||.|.+|+|.+++ +++++|||||+|.+.++|.+|++ +++..++||.|
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777778888777666            999999999999886 47899999999999999999998 89999999999


Q ss_pred             CCCCC
Q psy6490         233 DPKHA  237 (398)
Q Consensus       233 ~v~~~  237 (398)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            88765

>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=99.33  E-value=9e-13  Score=103.78  Aligned_cols=79  Identities=18%  Similarity=0.231  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCC--CCC---CHHHHHHHHhcCCCEEEEEEeeCCC----CCCcccEEEEEEcChHhHHHHHh-CCCcccCC
Q psy6490         160 TSAKLFVGGLS--WQT---SSEKLREYFGMFGAVTDVLIMKDPI----TQRSRGFGFITFAEPETVEKVLK-VPIHTLDG  229 (398)
Q Consensus       160 ~~~~l~v~nLp--~~~---t~~~L~~~f~~~G~i~~~~~~~~~~----~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g  229 (398)
                      ++++|+|+|+-  .++   .+++|++.|++||.|.+|+|.+++.    +++++||+||+|.+.++|.+|++ +|+..++|
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            67999999993  222   3689999999999999999999864    45788999999999999999998 89999999


Q ss_pred             cccCCCCCC
Q psy6490         230 KKIDPKHAT  238 (398)
Q Consensus       230 ~~l~v~~~~  238 (398)
                      |.|.+.+..
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999887764

>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=99.29  E-value=5.9e-12  Score=117.06  Aligned_cols=75  Identities=11%  Similarity=0.216  Sum_probs=61.7

Q ss_pred             CccccceeecC--CCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC---CE-
Q psy6490         246 GNRTKKIFVGG--VSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK---NK-  318 (398)
Q Consensus       246 ~~~~~~l~V~n--Lp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~---g~-  318 (398)
                      ..++++|||+|  |++.+||++|+++|++||.|++|++..      +||||||+|++.++|++|+ +|||+.+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45678999999  578999999999999999999887643      4899999999977776555 69999883   44 


Q ss_pred             -EEEEEecC
Q psy6490         319 -KVECKKAQ  326 (398)
Q Consensus       319 -~i~v~~a~  326 (398)
                       .|.|.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57778774

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.20  E-value=4.3e-11  Score=87.51  Aligned_cols=73  Identities=18%  Similarity=0.232  Sum_probs=60.9

Q ss_pred             cccceeecCCC----CCCCH----HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEE
Q psy6490         248 RTKKIFVGGVS----QDTSA----EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKK  319 (398)
Q Consensus       248 ~~~~l~V~nLp----~~~te----e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~  319 (398)
                      +..||+|.-.+    .++-.    .+|.+.|+.||.|..++++.|+        +||+|++.++|.+|++|||..++||.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            45567777665    23333    6789999999999999998873        89999999999999899999999999


Q ss_pred             EEEEecCch
Q psy6490         320 VECKKAQPK  328 (398)
Q Consensus       320 i~v~~a~~k  328 (398)
                      |+|+++++.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999998753

>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=99.19  E-value=2.1e-11  Score=113.31  Aligned_cols=63  Identities=16%  Similarity=0.245  Sum_probs=56.7

Q ss_pred             CCCcEEEEcC--CCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         159 PTSAKLFVGG--LSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       159 ~~~~~l~v~n--Lp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      .++++|||+|  |+.++||++|+++|++||+|.+|++..      +||||||+|.+.++|++|++ +|+..+
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~   81 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEV   81 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcc
Confidence            4789999999  588999999999999999999987753      48999999999999999998 888776

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=6.3e-11  Score=92.61  Aligned_cols=80  Identities=15%  Similarity=0.183  Sum_probs=67.1

Q ss_pred             CccccceeecCCCCC-CCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHH-HHHHHH--CCceeCCEEE
Q psy6490         246 GNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV-DHICEI--HFHMIKNKKV  320 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~-~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa-~a~~~l--~~~~i~g~~i  320 (398)
                      ......|||+||+.+ +++++|+++|+.||.|.+|.+.++..      .|||+|.+ .++| +++..+  ++..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            446778999999999 99999999999999999999988853      59999999 6555 556667  5888999999


Q ss_pred             EEEecCchHHH
Q psy6490         321 ECKKAQPKEAV  331 (398)
Q Consensus       321 ~v~~a~~k~~~  331 (398)
                      +++.....++.
T Consensus        89 ~~evL~GeeE~   99 (121)
T 1owx_A           89 TWEVLEGEVEK   99 (121)
T ss_dssp             EEEECCHHHHH
T ss_pred             EEEECCCHHHH
Confidence            99988766544

>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=99.13  E-value=5.1e-11  Score=93.03  Aligned_cols=75  Identities=11%  Similarity=0.137  Sum_probs=63.9

Q ss_pred             CCcEEEEcCCCCCC----------CHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccC
Q psy6490         160 TSAKLFVGGLSWQT----------SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLD  228 (398)
Q Consensus       160 ~~~~l~v~nLp~~~----------t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~  228 (398)
                      ++++|.+.|+=..-          -+++|++.|++||.|.+|.+.++.    ++||+||+|.+.++|.+|++ +|+..++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            67899999983322          235789999999999999997663    59999999999999999998 9999999


Q ss_pred             CcccCCCCCC
Q psy6490         229 GKKIDPKHAT  238 (398)
Q Consensus       229 g~~l~v~~~~  238 (398)
                      ||.|.+.+..
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999988764

>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=99.02  E-value=6e-10  Score=81.83  Aligned_cols=72  Identities=14%  Similarity=0.150  Sum_probs=60.5

Q ss_pred             ccccceeecCCCCC-----CCH----HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCC
Q psy6490         247 NRTKKIFVGGVSQD-----TSA----EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKN  317 (398)
Q Consensus       247 ~~~~~l~V~nLp~~-----~te----e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g  317 (398)
                      .+..||+|.-++.+     +-.    .+|.+.|+.||.|..++++.|+        +||+|.+.++|.+|++|||..++|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCC
Confidence            45668888887643     222    5689999999999999999883        999999999998888899999999


Q ss_pred             EEEEEEecC
Q psy6490         318 KKVECKKAQ  326 (398)
Q Consensus       318 ~~i~v~~a~  326 (398)
                      |.|+|++-.
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999999854

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=1.3e-09  Score=79.71  Aligned_cols=72  Identities=22%  Similarity=0.281  Sum_probs=61.7

Q ss_pred             CCcEEEEcCCCC----CCCH----HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcc
Q psy6490         160 TSAKLFVGGLSW----QTSS----EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKK  231 (398)
Q Consensus       160 ~~~~l~v~nLp~----~~t~----~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~  231 (398)
                      +..||+|.-.+.    ++-+    .+|.+.|+.||.|..++++.|+        +||+|.+.++|.+|+++++..++||.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            667888887762    3333    6688999999999999999873        89999999999999999999999999


Q ss_pred             cCCCCCCC
Q psy6490         232 IDPKHATP  239 (398)
Q Consensus       232 l~v~~~~~  239 (398)
                      |+|+..++
T Consensus        78 LkV~lkt~   85 (91)
T 2dnr_A           78 ITIALKSP   85 (91)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeCCC
Confidence            99987764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.92  E-value=8.7e-09  Score=77.01  Aligned_cols=73  Identities=8%  Similarity=0.111  Sum_probs=65.3

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhc-----CCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHCCceeCCEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQF-----GKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKV  320 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~-----G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa~a~~~l~~~~i~g~~i  320 (398)
                      +..++|-|-|||+.+++..|+.+.++|     |.|+++.+..|      -+-|+|+|.| ..++++.+.|+|..|+||+|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            346789999999999999999999999     99999999888      4579999999 46778889999999999999


Q ss_pred             EEEec
Q psy6490         321 ECKKA  325 (398)
Q Consensus       321 ~v~~a  325 (398)
                      +|.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            99754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=2.7e-09  Score=83.31  Aligned_cols=70  Identities=20%  Similarity=0.148  Sum_probs=58.3

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcC-hHhHHHHHh-C--CCcccCCcccC
Q psy6490         159 PTSAKLFVGGLSWQ-TSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE-PETVEKVLK-V--PIHTLDGKKID  233 (398)
Q Consensus       159 ~~~~~l~v~nLp~~-~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~-~e~a~~al~-~--~~~~~~g~~l~  233 (398)
                      .....|||+||+.+ +++++|+++|+.||.|..|.+.++..      .|||+|.+ .++|..|++ +  .+..|+|..+.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            47799999999999 99999999999999999999988753      59999999 788998887 4  34455555443


Q ss_pred             C
Q psy6490         234 P  234 (398)
Q Consensus       234 v  234 (398)
                      +
T Consensus        90 ~   90 (121)
T 1owx_A           90 W   90 (121)
T ss_dssp             E
T ss_pred             E
Confidence            3

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.88  E-value=3e-09  Score=93.70  Aligned_cols=72  Identities=18%  Similarity=0.173  Sum_probs=60.0

Q ss_pred             CCCHHHHHHHHhhcCCeeEEEEeecCC----CCCcceEEEEEeCCHHHHH-HHHHHCCceeCCEEEEEEecCchHHH
Q psy6490         260 DTSAEEVKAYFSQFGKVEETVMLMDQQ----TKRHRGFGFVTFENEEVVD-HICEIHFHMIKNKKVECKKAQPKEAV  331 (398)
Q Consensus       260 ~~tee~L~~~F~~~G~i~~v~i~~~~~----~~~~kg~afV~F~~~eaa~-a~~~l~~~~i~g~~i~v~~a~~k~~~  331 (398)
                      +-.+++|++.|++||.|.++.|.++..    +++++|++||+|.+.++|. |+..|||..++||.|+|.++....-+
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~f~  216 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFD  216 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHHHH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHHhh
Confidence            446789999999999999999986644    4589999999999977665 55579999999999999998765433

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=6.5e-09  Score=76.33  Aligned_cols=71  Identities=21%  Similarity=0.268  Sum_probs=61.2

Q ss_pred             CCcEEEEcCCCCC------CCH---HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCc
Q psy6490         160 TSAKLFVGGLSWQ------TSS---EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGK  230 (398)
Q Consensus       160 ~~~~l~v~nLp~~------~t~---~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~  230 (398)
                      +..||+|.-++.+      ..+   .+|.+.|+.||+|..++++.|+        +||+|.+.++|.+||++++..++||
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~Gr   85 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKGR   85 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETTE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCCe
Confidence            6789999988643      232   5688999999999999999883        9999999999999999999999999


Q ss_pred             ccCCCCCC
Q psy6490         231 KIDPKHAT  238 (398)
Q Consensus       231 ~l~v~~~~  238 (398)
                      .|+|+...
T Consensus        86 ~L~V~~k~   93 (95)
T 1ufw_A           86 AVKISGPS   93 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeccC
Confidence            99987654

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.65  E-value=2.5e-08  Score=87.73  Aligned_cols=79  Identities=18%  Similarity=0.226  Sum_probs=64.4

Q ss_pred             CCcEEEEcCCCC-----CCCHHHHHHHHhcCCCEEEEEEeeCCC----CCCcccEEEEEEcChHhHHHHHh-CCCcccCC
Q psy6490         160 TSAKLFVGGLSW-----QTSSEKLREYFGMFGAVTDVLIMKDPI----TQRSRGFGFITFAEPETVEKVLK-VPIHTLDG  229 (398)
Q Consensus       160 ~~~~l~v~nLp~-----~~t~~~L~~~f~~~G~i~~~~~~~~~~----~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g  229 (398)
                      ..+.+.+.|+-.     +-.+++|++.|++||.|.++++.++..    +++++|++||+|.+.++|.+|++ +++..++|
T Consensus       123 ~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~g  202 (222)
T 3dxb_A          123 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG  202 (222)
T ss_dssp             BCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             ccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECC
Confidence            344555555522     345688999999999999999986543    45899999999999999999998 99999999


Q ss_pred             cccCCCCCC
Q psy6490         230 KKIDPKHAT  238 (398)
Q Consensus       230 ~~l~v~~~~  238 (398)
                      |.|.+.+..
T Consensus       203 r~i~~~~~~  211 (222)
T 3dxb_A          203 RKVVAEVYD  211 (222)
T ss_dssp             SBCEEEECC
T ss_pred             eEEEEEEcC
Confidence            999887764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.50  E-value=1.5e-06  Score=64.49  Aligned_cols=88  Identities=28%  Similarity=0.408  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhc---C--CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGM---F--GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP  234 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~---~--G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v  234 (398)
                      -..+|.|.|||.+++++.|.-+|++   -  |+|.++....        +-|+|+|.+.+.+++.|+...+.|++..|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            5689999999999999999999986   2  4888887744        3699999999999999998788999999988


Q ss_pred             CCCCCCCCCccCccccceeecCCCCCCC
Q psy6490         235 KHATPKNRPKIGNRTKKIFVGGVSQDTS  262 (398)
Q Consensus       235 ~~~~~~~~~~~~~~~~~l~V~nLp~~~t  262 (398)
                      .....+.       ..+|++.+|+..++
T Consensus        79 ~P~~~~~-------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           79 RPAPPRA-------PARLLLQGLPPGTS   99 (104)
T ss_dssp             EECCCCC-------CCCCCCCSCCCCCC
T ss_pred             EcCCCCC-------cceEeeecCCCCCC
Confidence            7765443       46799999998875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.20  E-value=1.3e-05  Score=59.59  Aligned_cols=91  Identities=20%  Similarity=0.253  Sum_probs=74.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhh-c----CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQ-F----GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~-~----G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v  322 (398)
                      ..++|.|.|||.++++|.|.-+|+. .    |.|+++....        +-|+|+|.+.+.++.+++...+.|.+..|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            4578999999999999999999997 2    5788776643        3789999999999999998899999999999


Q ss_pred             EecCchHHHhhhhhcCCccccCCCCCCCCCCC
Q psy6490         323 KKAQPKEAVQANLLVGKRVILGPLGLRMAAPA  354 (398)
Q Consensus       323 ~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (398)
                      .-..++        ..++.++.++...+..+.
T Consensus        79 ~P~~~~--------~~~r~ll~gl~~~t~~~~  102 (104)
T 2dhx_A           79 RPAPPR--------APARLLLQGLPPGTSGPS  102 (104)
T ss_dssp             EECCCC--------CCCCCCCCSCCCCCCCCC
T ss_pred             EcCCCC--------CcceEeeecCCCCCCCCC
Confidence            876655        346777777777776553

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.20  E-value=2.4e-06  Score=63.92  Aligned_cols=70  Identities=17%  Similarity=0.193  Sum_probs=62.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcC-----CCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHH-hCCCcccCCcccC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMF-----GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KVPIHTLDGKKID  233 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~-----G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al-~~~~~~~~g~~l~  233 (398)
                      ..++|-+-|||..+++..|+.+++.+     |.|+.+.+..|.      +-|+|+|.|..+|-+|. .+++.+|.||+|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            57899999999999999999999999     999999999984      45999999999988875 7999999999886


Q ss_pred             CC
Q psy6490         234 PK  235 (398)
Q Consensus       234 v~  235 (398)
                      +.
T Consensus        94 ~g   95 (117)
T 2l9w_A           94 SG   95 (117)
T ss_dssp             EE
T ss_pred             ec
Confidence            54

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.70  E-value=8.2e-05  Score=55.54  Aligned_cols=74  Identities=15%  Similarity=0.108  Sum_probs=58.5

Q ss_pred             ccceeecCCCCCC-C----HHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEEE
Q psy6490         249 TKKIFVGGVSQDT-S----AEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVEC  322 (398)
Q Consensus       249 ~~~l~V~nLp~~~-t----ee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~v  322 (398)
                      .++|+|.||+.++ +    .+.++++|..|+++.....++.-      .-..|.|.+.++| ++-++||+..+.|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4679999998765 2    25778999999998887776552      2568999996555 555689999999999999


Q ss_pred             EecCch
Q psy6490         323 KKAQPK  328 (398)
Q Consensus       323 ~~a~~k  328 (398)
                      -++.+-
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            999843

>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=97.65  E-value=0.00027  Score=54.25  Aligned_cols=79  Identities=14%  Similarity=0.175  Sum_probs=64.3

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCC-EEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKN-KKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g-~~i~v~~a  325 (398)
                      ...+.|.|-+.+... .+.|.+.|++||.|.+....    .+  ..+-.|+|++..+|++|+..||..|+| -.|-|.++
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            346789999998885 67788899999999987751    12  459999999999999999999999984 78889988


Q ss_pred             CchHHHh
Q psy6490         326 QPKEAVQ  332 (398)
Q Consensus       326 ~~k~~~~  332 (398)
                      ..+.-..
T Consensus        95 ~d~~vi~  101 (119)
T 1wwh_A           95 IDKNVME  101 (119)
T ss_dssp             CCHHHHC
T ss_pred             CCHHHHH
Confidence            7665443

>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=97.46  E-value=0.00047  Score=50.53  Aligned_cols=53  Identities=21%  Similarity=0.374  Sum_probs=43.3

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE  309 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~  309 (398)
                      ....++| +.|.++...||.++|+.||.|. |+.+-|.       -|||.|.+.+.|..++.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT-------sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            3455666 9999999999999999999766 5555552       79999999998887776

>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=97.44  E-value=0.00042  Score=50.81  Aligned_cols=67  Identities=7%  Similarity=0.125  Sum_probs=52.5

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR--HRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~--~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      ++|.|++||..+||+++.+.++.+..+.....+..+.+.+  .-..|||.|.+.|++.... .++|+.+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4799999999999999999999998888777665543322  2357999999977776655 68888764

>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=97.37  E-value=0.00062  Score=49.91  Aligned_cols=66  Identities=12%  Similarity=0.095  Sum_probs=52.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCC--cccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR--SRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~--~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      ++|.|++||.++||+++.+.++.+.++.....+..+.+.+  .-.-|||.|.+.+++....+ .++..+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            5789999999999999999999998887777766554332  23459999999999998876 455554

>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=97.34  E-value=0.00088  Score=49.11  Aligned_cols=53  Identities=21%  Similarity=0.437  Sum_probs=45.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ....++| ++|.++...||.++|+.||.| .|+.+.|.       .|||.|.+++.|..|++
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            5567777 999999999999999999954 46666663       79999999999999987

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.30  E-value=0.00071  Score=51.94  Aligned_cols=73  Identities=12%  Similarity=0.132  Sum_probs=58.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCC-cccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDG-KKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g-~~l~v~~  236 (398)
                      ....+.|.|-+.|.+. ...|.+.|++||.|++.....      ...+-.|.|.+..+|++||..|+..++| ..|-|.+
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKP   93 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEE
Confidence            3467899999999985 566888899999999887621      2569999999999999999999999875 4455554


Q ss_pred             C
Q psy6490         237 A  237 (398)
Q Consensus       237 ~  237 (398)
                      .
T Consensus        94 ~   94 (119)
T 1wwh_A           94 C   94 (119)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=97.07  E-value=0.00066  Score=50.64  Aligned_cols=73  Identities=18%  Similarity=0.149  Sum_probs=60.5

Q ss_pred             CcEEEEcCCCCCC-CH----HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         161 SAKLFVGGLSWQT-SS----EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       161 ~~~l~v~nLp~~~-t~----~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .++|+|.||+.++ +.    +.++++|..|+++......+.-     + -..|.|.+.++|.+|-. +++..++|++|++
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            4789999998875 22    5678999999999888887753     2 57999999999999965 8999999999988


Q ss_pred             CCCCC
Q psy6490         235 KHATP  239 (398)
Q Consensus       235 ~~~~~  239 (398)
                      ..+..
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            87763

>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=97.01  E-value=0.00055  Score=50.34  Aligned_cols=52  Identities=19%  Similarity=0.349  Sum_probs=42.0

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE  309 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~  309 (398)
                      ...++| +.|.++...||.++|+.||.|. |+.+-|.       -|||.|.+.+.|+.++.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv~-I~WidDT-------sAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEEE-EEEEETT-------EEEEEEEEECHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCEE-EEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            445666 9999999999999999999655 5555552       79999999888877765

>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=96.98  E-value=0.0013  Score=48.30  Aligned_cols=52  Identities=21%  Similarity=0.408  Sum_probs=44.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ...++| ++|.++...||.++|+.|| -..|+.+.|.       .|||.|.+++.|..|++
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            355666 9999999999999999999 4456677764       79999999999999987

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.82  E-value=0.0017  Score=50.52  Aligned_cols=79  Identities=18%  Similarity=0.226  Sum_probs=57.2

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEE-EeecC--------CCC-----CcceEEEEEeCCHHHHHHHHHHCCce
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV-MLMDQ--------QTK-----RHRGFGFVTFENEEVVDHICEIHFHM  314 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~-i~~~~--------~~~-----~~kg~afV~F~~~eaa~a~~~l~~~~  314 (398)
                      ...|.|-+.|.+. ...|.+.|++||.|.+-. ..++.        ...     ...+|..|+|++..+|.+|+..||..
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            4557788886665 456778899999987621 11100        000     12568899999999999999999999


Q ss_pred             eCCEEEEEEecCch
Q psy6490         315 IKNKKVECKKAQPK  328 (398)
Q Consensus       315 i~g~~i~v~~a~~k  328 (398)
                      |+|..|-|.++++.
T Consensus        86 i~G~mIGV~Py~~~   99 (132)
T 3p3d_A           86 FNGVLLGVIPYTKD   99 (132)
T ss_dssp             ETTEECEEEECCHH
T ss_pred             eCcEEEEEEECCHH
Confidence            99999999998643

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.52  E-value=0.0025  Score=61.22  Aligned_cols=57  Identities=12%  Similarity=0.314  Sum_probs=44.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV  222 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~  222 (398)
                      ..++|||. .+.++++++|.++|++||.|.++.+-+++     .-|+.|+|.+.+++..++..
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            46899998 79999999999999999999999887764     46999999999999988764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.27  E-value=0.0032  Score=46.36  Aligned_cols=69  Identities=4%  Similarity=0.070  Sum_probs=47.3

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR--HRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~--~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      .+-+|.|+.||..+||+++.+.++..-.+.....+..+.+.+  .-..|||.|.+.|+..... ..+|..+-
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            345799999999999999988888765554433322221111  1245899999988777655 57887764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.25  E-value=0.0041  Score=45.85  Aligned_cols=68  Identities=13%  Similarity=0.103  Sum_probs=47.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCC--cccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR--SRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~--~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      .+-.|.|+.||+.+||+++.+.++.+-++.....+..+.+.+  .-..|||.|.+.++.....+ .++..+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            467899999999999999988887665543333322222211  12359999999999999877 555554

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.10  E-value=0.0023  Score=61.43  Aligned_cols=59  Identities=15%  Similarity=0.308  Sum_probs=43.3

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHF  312 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~  312 (398)
                      ..++|+|. .+.++++.+|.++|+.||.|.++.+.+++     .-||.|+|.+.+++.++++..+
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~~  110 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGTH  110 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSCC
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhccC
Confidence            45679998 79999999999999999999988776542     3699999999998888875433

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.94  E-value=0.0029  Score=49.25  Aligned_cols=77  Identities=14%  Similarity=0.255  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEE-EeeC------------CCCC-CcccEEEEEEcChHhHHHHHhCCCc
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-IMKD------------PITQ-RSRGFGFITFAEPETVEKVLKVPIH  225 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~-~~~~------------~~~~-~~~g~afV~f~~~e~a~~al~~~~~  225 (398)
                      ....|.|-+.|.+.+.. +.+.|++||.|.+-. +.++            +... ....+..|.|.+..+|.+||..|+.
T Consensus         6 ~e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~   84 (132)
T 3p3d_A            6 GELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGA   84 (132)
T ss_dssp             --CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTC
T ss_pred             CceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCe
Confidence            44677788887766554 677899999987621 1110            0000 1356789999999999999999999


Q ss_pred             ccCCcccCCCCC
Q psy6490         226 TLDGKKIDPKHA  237 (398)
Q Consensus       226 ~~~g~~l~v~~~  237 (398)
                      .++|.-|-|.+.
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999976655544

>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=88.11  E-value=1.4  Score=43.03  Aligned_cols=53  Identities=21%  Similarity=0.367  Sum_probs=41.1

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE  309 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~  309 (398)
                      +...++|+ ++..+...+|.++|+.||.|. |+.+-|       ..|||.|.+.+.+..++.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v~-V~widd-------t~a~V~~~~~~~a~~~l~  491 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNIQ-ISWIDD-------TSAFVSLSQPEQVQIAVN  491 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCCE-EEECSS-------SEEEEECSCHHHHHHHHH
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCEE-EEEEcC-------CeEEEEECCHHHHHHHHH
Confidence            34556666 899999999999999999654 554433       279999999988877664

>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=86.87  E-value=1.3  Score=43.09  Aligned_cols=53  Identities=21%  Similarity=0.429  Sum_probs=43.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ....++|+ ++..+...+|.++|+.||.+ +|+.+.|       ..+||.|.+.+.|..+++
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~  491 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVN  491 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHH
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHH
Confidence            45677787 99999999999999999954 4555544       269999999999999887

---

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	398
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-33
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-13
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-21
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-20
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-21
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-19
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-21
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-18
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-20
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-19
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-19
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-19
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-19
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-18
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-18
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-18
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	9e-17
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-17
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-17
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-17
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	8e-16
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-15
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-15
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-13
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	9e-14
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-14
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-12
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-12
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-11
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	6e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	9e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	9e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-09
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-10
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	9e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.001
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.003
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.002
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.002
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.004

>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 =  121 bits (304), Expect = 1e-33
 Identities = 67/170 (39%), Positives = 106/170 (62%), Gaps = 3/170 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 223 PIHTLDGKKIDPKHATPKNRPKIGN---RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEET 279
             H +DG+ ++PK A  +   +        KKIFVGG+ +DT    ++ YF Q+GK+E  
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127

Query: 280 VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            ++ D+ + + RGF FVTF++ + VD I    +H +     E +KA  K+
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 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 = 66.2 bits (160), Expect = 2e-13
 Identities = 30/79 (37%), Positives = 50/79 (63%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E VD    
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 310 IHFHMIKNKKVECKKAQPK 328
              H +  + VE K+A  +
Sbjct: 67  ARPHKVDGRVVEPKRAVSR 85

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (159), Expect = 3e-13
 Identities = 28/85 (32%), Positives = 47/85 (55%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
              T  K+FVGG+   T    LR+YF  +G +  + IM D  + + RGF F+TF + ++V
Sbjct: 93  AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152

Query: 217 EKVLKVPIHTLDGKKIDPKHATPKN 241
           +K++    HT++G   + + A  K 
Sbjct: 153 DKIVIQKYHTVNGHNCEVRKALSKQ 177

>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 = 85.0 bits (210), Expect = 2e-21
 Identities = 35/75 (46%), Positives = 46/75 (61%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T  EK+REYFG FG V  + +  D  T + RGF FITF E E V+K+++ 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 223 PIHTLDGKKIDPKHA 237
             H +   K + K A
Sbjct: 61  KYHNVGLSKCEIKVA 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 = 83.1 bits (205), Expect = 1e-20
 Identities = 35/75 (46%), Positives = 47/75 (62%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S DT  E+++ YF  FG+VE   + MD +T + RGF F+TF+ EE V  I E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 311 HFHMIKNKKVECKKA 325
            +H +   K E K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 84.3 bits (208), Expect = 4e-21
 Identities = 46/75 (61%), Positives = 57/75 (76%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF +   V+KVL  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 223 PIHTLDGKKIDPKHA 237
             H LD K IDPK A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 79.3 bits (195), Expect = 3e-19
 Identities = 32/75 (42%), Positives = 50/75 (66%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S  T+ E ++ YF QFG+V+E +++ D  TKR RGFGFVTF ++  VD +   
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 311 HFHMIKNKKVECKKA 325
             H + +K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 83.5 bits (206), Expect = 9e-21
 Identities = 41/75 (54%), Positives = 53/75 (70%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+F+GGLSW T+ + L++YF  FG V D  +  DPIT RSRGFGF+ F E E+V+KV+  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 223 PIHTLDGKKIDPKHA 237
             H L+GK IDPK A
Sbjct: 61  KEHKLNGKVIDPKRA 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 = 76.2 bits (187), Expect = 4e-18
 Identities = 31/75 (41%), Positives = 50/75 (66%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+F+GG+S DT+ +++K YFS+FG+V +  + +D  T R RGFGFV F+  E VD + + 
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 311 HFHMIKNKKVECKKA 325
             H +  K ++ K+A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.5 bits (206), Expect = 1e-20
 Identities = 34/80 (42%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           ++ L V GL W+T+ + L+EYF  FG V  V + KD  T  S+GFGF+ F E ET  KV+
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 221 KVPIHTLDGKKIDPKHATPK 240
               H +DG+  D K    K
Sbjct: 68  SQR-HMIDGRWCDCKLPNSK 86

>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 = 80.4 bits (198), Expect = 2e-19
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
           +T  + V G+   T+ +++K YFS FG+V    +  D +T   +GFGFV F   E    +
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
                HMI  +  +CK    K+
Sbjct: 67  MS-QRHMIDGRWCDCKLPNSKQ 87

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 80.5 bits (198), Expect = 2e-19
 Identities = 34/78 (43%), Positives = 56/78 (71%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR Y+  +G +TD ++M+DP ++RSRGFGF+TF+    V+  +  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 81

Query: 223 PIHTLDGKKIDPKHATPK 240
             H++DG+ ++PK A  +
Sbjct: 82  RPHSIDGRVVEPKRAVAR 99

>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 = 80.5 bits (198), Expect = 2e-19
 Identities = 32/91 (35%), Positives = 55/91 (60%)

Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
            + + +   + +K+F+GG+S +T+ E ++ Y+ Q+GK+ + V++ D  +KR RGFGFVTF
Sbjct: 10  LERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 69

Query: 299 ENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            +   VD       H I  + VE K+A  +E
Sbjct: 70  SSMAEVDAAMAARPHSIDGRVVEPKRAVARE 100

>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 = 78.9 bits (194), Expect = 5e-19
 Identities = 36/75 (48%), Positives = 55/75 (73%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KLF+GGLS++T+ E LR +F  +G +TD ++M+DP T+RSRGFGF+T+A  E V+  +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 223 PIHTLDGKKIDPKHA 237
             H +DG+ ++PK A
Sbjct: 68  RPHKVDGRVVEPKRA 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 = 77.4 bits (190), Expect = 2e-18
 Identities = 30/77 (38%), Positives = 49/77 (63%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
            +K+F+GG+S +T+ E ++++F Q+G + + V++ D  TKR RGFGFVT+   E VD   
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 309 EIHFHMIKNKKVECKKA 325
               H +  + VE K+A
Sbjct: 66  NARPHKVDGRVVEPKRA 82

>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 = 78.2 bits (192), Expect = 1e-18
 Identities = 32/87 (36%), Positives = 51/87 (58%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           D T  K+FVGGL + T+   LR+YF  FG + + +++ D  T +SRG+GF+T A+    E
Sbjct: 7   DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRPK 244
           +  K P   +DG+K +   A    +P+
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

>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 = 62.1 bits (150), Expect = 8e-13
 Identities = 27/80 (33%), Positives = 42/80 (52%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
             KIFVGG+   T+   ++ YF  FG +EE V++ D+QT + RG+GFVT  +    +  C
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 309 EIHFHMIKNKKVECKKAQPK 328
           +    +I  +K     A   
Sbjct: 70  KDPNPIIDGRKANVNLAYLG 89

>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 = 78.1 bits (192), Expect = 1e-18
 Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 1/100 (1%)

Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
           KS         + ++  +  +F   L+ +     L ++F   G V DV I+ D  ++RS+
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP-KNR 242
           G  ++ F E ++V   + +    L G  I  + +   KNR
Sbjct: 61  GIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 73.1 bits (179), Expect = 8e-17
 Identities = 15/96 (15%), Positives = 39/96 (40%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
           P      N        + +F   ++      +++ +FS  GKV +  ++ D+ ++R +G 
Sbjct: 3   PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 62

Query: 294 GFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            +V F   + V     +    +    +  + +Q ++
Sbjct: 63  AYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK 98

>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 = 76.1 bits (187), Expect = 6e-18
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 3/90 (3%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGFGFITFAEPETV 216
             T++K+ V  + +Q +  ++RE F  FG +  V + K    T   RGFGF+ F   +  
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 217 EKVLKVPIH--TLDGKKIDPKHATPKNRPK 244
           +K      H   L G+++  + A  +   +
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 72.7 bits (178), Expect = 9e-17
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 3/89 (3%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGFGFVTFENEEVVD 305
             T KI V  +    +  E++  FS FG+++   +      T  HRGFGFV F  ++   
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 306 HICE--IHFHMIKNKKVECKKAQPKEAVQ 332
                  H   +  +++  + A  +  VQ
Sbjct: 66  KAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 74.4 bits (182), Expect = 2e-17
 Identities = 30/76 (39%), Positives = 47/76 (61%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
           KKIFVGG+ +DT    ++ YF Q+GK+E   ++ D+ + + RGF FVTF++ + VD I  
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 310 IHFHMIKNKKVECKKA 325
             +H +     E +KA
Sbjct: 63  QKYHTVNGHNCEVRKA 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 = 72.8 bits (178), Expect = 7e-17
 Identities = 27/78 (34%), Positives = 46/78 (58%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           T  K+FVGG+   T    LR+YF  +G +  + IM D  + + RGF F+TF + ++V+K+
Sbjct: 1   TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 60

Query: 220 LKVPIHTLDGKKIDPKHA 237
           +    HT++G   + + A
Sbjct: 61  VIQKYHTVNGHNCEVRKA 78

>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 = 72.8 bits (178), Expect = 6e-17
 Identities = 34/75 (45%), Positives = 48/75 (64%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           K+FVGGLS  T+ E ++ YF  FG V D ++M D  T R RGFGF+TF   + VEKV ++
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 223 PIHTLDGKKIDPKHA 237
             H ++ K ++ K A
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 = 72.1 bits (176), Expect = 1e-16
 Identities = 48/75 (64%), Positives = 63/75 (84%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           KIFVGG+S +T+ E+VK YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEI
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 311 HFHMIKNKKVECKKA 325
           HFH I NK VECKKA
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 70.3 bits (172), Expect = 5e-16
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+VG L    +   L E F   G +  + + +D IT+RS G+ ++ F +P   E+ L 
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 222 VPIHTLDGKKID 233
               T++   I 
Sbjct: 61  ----TMNFDVIK 68

>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 = 66.9 bits (163), Expect = 8e-15
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
            ++VG +  D +   +   FS  G +    +  D  T+R  G+ +V F+     +  +  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 310 IHFHMIKNKKVECKKAQ 326
           ++F +IK K V    +Q
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 70.1 bits (171), Expect = 8e-16
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
           P  +    A ++VGGL  + S   L E F   G V +  + KD +T + +G+GF+ F   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 214 ETVEKVLK-VPIHTLDGKKIDPKHATPKNR 242
           E  +  +K + +  L GK I    A+  N+
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 67.0 bits (163), Expect = 1e-14
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           N+   ++VGG+ +  S   +   F Q G V  T M  D+ T +H+G+GFV F +EE  D+
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 307 -ICEIHFHMIKNKKVECKKAQPKE 329
            I  +    +  K +   KA    
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAHN 90

>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 = 70.3 bits (172), Expect = 1e-15
 Identities = 17/102 (16%), Positives = 35/102 (34%), Gaps = 10/102 (9%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
           G SG S  T     ++++F+G L+        +   F  +G +    +         +GF
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGF 52

Query: 206 GFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPKIG 246
            F+ +         +       + G+ +D   A      + G
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSG 94

>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 = 62.2 bits (151), Expect = 7e-13
 Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 10/91 (10%)

Query: 241 NRPKIGNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
            +    +   ++F+G ++       +V+A FS++GK+             H+GF FV + 
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVG--------CSVHKGFAFVQYV 58

Query: 300 NEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
           NE      +      MI  + ++   A   +
Sbjct: 59  NERNARAAVAGEDGRMIAGQVLDINLAAEPK 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 = 69.2 bits (169), Expect = 2e-15
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           G+      L+V  L    + ++L   FG +G++    I++D +T R RG  F+ + + E 
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 216 VEKVLKVPIHTLDGKKID 233
            ++     I  L+    +
Sbjct: 61  AQEA----ISALNNVIPE 74

>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 = 60.7 bits (147), Expect = 1e-12
 Identities = 14/81 (17%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
           +   ++V  + +  + +++   F ++G + +  +L D+ T R RG  FV +   E     
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 307 ICEIHFHMIK--NKKVECKKA 325
           I  ++  + +  ++ +  + A
Sbjct: 65  ISALNNVIPEGGSQPLSVRLA 85

>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 = 69.0 bits (168), Expect = 3e-15
 Identities = 25/105 (23%), Positives = 43/105 (40%), Gaps = 3/105 (2%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG   P    P     F+G L +  + E ++E+F         L  +    +R +G
Sbjct: 2   SSGSSGSRLP--KSPPY-TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKG 58

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
           FG+  F + +++   L +   +L  K+I    A        G  +
Sbjct: 59  FGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 57.8 bits (139), Expect = 3e-11
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 2/93 (2%)

Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
           ++    PK    T   F+G +  D + E +K +F         +       +R +GFG+ 
Sbjct: 5   SSGSRLPKSPPYT--AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA 62

Query: 297 TFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
            FE+ + +     ++   + NK++    A   +
Sbjct: 63  EFEDLDSLLSALSLNEESLGNKRIRVDVADQAQ 95

>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 = 68.1 bits (166), Expect = 4e-15
 Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
           + ++VGG++++   + + A F  FG + +  + +D +T++HRGF FV FE  E     I 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
            ++   +  + +    A+P  
Sbjct: 66  NMNESELFGRTIRVNLAKPMR 86

>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 = 66.2 bits (161), Expect = 2e-14
 Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
            T   L+VGGL+ +   + L   F  FG +TD+ I  D  T++ RGF F+ F   E    
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 219 VLKVP-IHTLDGKKIDPKHATPKNRPK 244
            +       L G+ I    A P  R K
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPM-RIK 88

>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 = 67.7 bits (165), Expect = 5e-15
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           + KLF+GGL    + ++++E    FG +    ++KD  T  S+G+ F  + +    ++ +
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 221 KVPI-HTLDGKKIDPKHATPKNR 242
                  L  KK+  + A+   +
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAK 83

>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 = 63.9 bits (155), Expect = 1e-13
 Identities = 18/79 (22%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           K+F+GG+    + ++VK   + FG ++   ++ D  T   +G+ F  + +  V D  I  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 310 IHFHMIKNKKVECKKAQPK 328
           ++   + +KK+  ++A   
Sbjct: 63  LNGMQLGDKKLLVQRASVG 81

>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 = 6e-15
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAV-TDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
           +F+G L  +   + L + F  FG +     IM+DP T  S+G+ FI FA  +  +  ++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 222 VPIHTLDGKKIDPKHATPKN 241
           +    L  + I   +A  K+
Sbjct: 61  MNGQYLCNRPITVSYAFKKD 80

>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 = 66.7 bits (162), Expect = 1e-14
 Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM-DQQTKRHRGFGFVTFENEEVVDH-ICE 309
           IF+G +  +   + +   FS FG + +T  +M D  T   +G+ F+ F + +  D  I  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 310 IHFHMIKNKKVECKKAQPKE 329
           ++   + N+ +    A  K+
Sbjct: 61  MNGQYLCNRPITVSYAFKKD 80

>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 = 7e-15
 Identities = 17/87 (19%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
           K+  ++  ++VG +S  T+ E++   FS+ G +++ +M +D+  K   GF FV + +   
Sbjct: 2   KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 61

Query: 304 VDH-ICEIHFHMIKNKKVECKKAQPKE 329
            ++ +  I+   + ++ +        +
Sbjct: 62  AENAMRYINGTRLDDRIIRTDWDAGFK 88

>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 = 64.6 bits (157), Expect = 8e-14
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           S  L+VG LS+ T+ E++ E F   G +  +++  D + + + GF F+ +      E  +
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 221 KVPIHTLDGKKID 233
           +     ++G ++D
Sbjct: 67  R----YINGTRLD 75

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
              S+ +FVG  +   + ++LRE+F  +G V DV I      +  R F F+TFA+ +  +
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQ 56

Query: 218 KVLKVPIHTLDGKKIDPKHATPKN 241
            +       + G  +   +A PK+
Sbjct: 57  SLCGED-LIIKGISVHISNAEPKH 79

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 5e-13
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
           +  +FVG  + D + +E++ +FSQ+G V +  +         R F FVTF ++++   +C
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLC 59

Query: 309 EIHFHMIKNKKVECKKAQPKE 329
                +IK   V    A+PK 
Sbjct: 60  G-EDLIIKGISVHISNAEPKH 79

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.2 bits (158), Expect = 4e-14
 Identities = 27/80 (33%), Positives = 51/80 (63%), Gaps = 1/80 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           K+FVGG+S DT+ + ++  FS++G++ E V++ D++T+R RGFGFVTFEN +     +  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 310 IHFHMIKNKKVECKKAQPKE 329
           ++   +  +++   +A    
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>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 = 63.6 bits (154), Expect = 1e-13
 Identities = 30/85 (35%), Positives = 52/85 (61%), Gaps = 1/85 (1%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
             KLFVGGLS+ T+ + L + F  +G +++V+++KD  TQRSRGFGF+TF   +  +  +
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 221 K-VPIHTLDGKKIDPKHATPKNRPK 244
             +   ++DG++I    A   +  +
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSDNR 89

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.1 bits (158), Expect = 5e-14
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 4/84 (4%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP---ITQRSRGFGFITFAEPETVEKVL 220
           LF+  L++ T+ E L+  F   GA+    I K         S GFGF+ + +PE  +K L
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 221 KVPI-HTLDGKKIDPKHATPKNRP 243
           K    HT+DG K++ + +    +P
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>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 = 64.3 bits (156), Expect = 9e-14
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ---QTKRHRGFGFVTFENEEVVDH-I 307
           +F+  ++  T+ E +K  FS+ G ++   +   +         GFGFV ++  E     +
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
            ++  H +   K+E + ++   
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>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 = 65.1 bits (158), Expect = 7e-14
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 1/101 (0%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           +    G +    + P  A LF+  L  +   + L + F  FG V    +  D  T  S+ 
Sbjct: 2   TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 61

Query: 205 FGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK 244
           FGF+++  P + +  ++ +    +  K++  +    KN  K
Sbjct: 62  FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 55.9 bits (134), Expect = 1e-10
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFG 294
           +        K G     +F+  + Q+   +++   F  FG V    + +D+QT   + FG
Sbjct: 4   QSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 63

Query: 295 FVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
           FV+++N       I  ++   I  K+++ +  + K 
Sbjct: 64  FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 64.3 bits (156), Expect = 7e-14
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
           A L+V GL    + ++L + F  +G +    I+ D +T  SRG GFI F +    E+   
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA-- 64

Query: 222 VPIHTLDGKKIDPKH 236
             I  L+G+K     
Sbjct: 65  --IKGLNGQKPSGAT 77

>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 = 62.0 bits (150), Expect = 6e-13
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
           R   ++V G+ +  + +E++  FSQ+G++  + +L+DQ T   RG GF+ F+     +  
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 307 ICEIHFHMI--KNKKVECKKA 325
           I  ++        + +  K A
Sbjct: 65  IKGLNGQKPSGATEPITVKFA 85

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 28/99 (28%), Positives = 50/99 (50%), Gaps = 9/99 (9%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG+S          T  +L V  + ++     LR+ FG FG + DV I+ +   + S+G
Sbjct: 1   SSGNSE------SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKG 52

Query: 205 FGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNR 242
           FGF+TF      ++  + +    ++G+KI+  +AT +  
Sbjct: 53  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 91

>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 = 58.5 bits (141), Expect = 1e-11
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 3/81 (3%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
            K++ V  +       +++  F QFGK+ +  ++ +++  +   FGFVTFEN    D   
Sbjct: 11  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSADADRAR 68

Query: 308 CEIHFHMIKNKKVECKKAQPK 328
            ++H  +++ +K+E   A  +
Sbjct: 69  EKLHGTVVEGRKIEVNNATAR 89

>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 = 64.0 bits (155), Expect = 2e-13
 Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 11/101 (10%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG          S +LFV  LS+ +S E L + F  +G ++++    D +T++ +G
Sbjct: 2   SSGSSG----------SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG 51

Query: 205 FGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPK 244
           F F+TF  PE   K    V      G+ +    +T K    
Sbjct: 52  FAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 57.0 bits (137), Expect = 4e-11
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
           + ++FV  +S  +S E+++  FS +G + E    +D  TK+ +GF FVTF   E      
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
            E+   + + + +    +  K+
Sbjct: 68  AEVDGQVFQGRMLHVLPSTIKK 89

>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 = 63.6 bits (154), Expect = 2e-13
 Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 5/87 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTD--VLIMKDPITQRSRGFGFITFAEPETVEKVL 220
           +LF+GG+      E++ E            ++        ++RGF F+ +          
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 221 KV---PIHTLDGKKIDPKHATPKNRPK 244
           +        L G +I    A P+    
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVD 89

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 6e-13
 Identities = 15/91 (16%), Positives = 36/91 (39%), Gaps = 5/91 (5%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETV--MLMDQQTKRHRGFGFVTFENEEVVDHIC 308
           ++F+GG+ +    EE+    ++  +    V          ++RGF FV +E+        
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 309 EI---HFHMIKNKKVECKKAQPKEAVQANLL 336
                    +   ++    A+P+  V  +++
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVM 93

>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 = 62.8 bits (152), Expect = 3e-13
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +   +  L V GLS  T+   LRE F  +G + DV I+ D  ++RSRGF F+ F   +  
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

Query: 217 EKVLKVPIHTLDGKKIDPK 235
           ++         +G ++D +
Sbjct: 65  KEA----KERANGMELDGR 79

>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 = 7e-12
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 246 GNR-----TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           GNR        + V G+S  T+  +++  FS++G + +  ++ DQQ++R RGF FV FEN
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 301 EEVVDH-ICEIHFHMIKNKKVE 321
            +         +   +  +++ 
Sbjct: 61  VDDAKEAKERANGMELDGRRIR 82

>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 = 60.9 bits (147), Expect = 1e-12
 Identities = 9/86 (10%), Positives = 29/86 (33%), Gaps = 5/86 (5%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLI-----MKDPITQRSRGFGFITFAEPETVE 217
           +L+VG + +  + E + ++F     +  +       +      + + F F+ F   +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRP 243
           + +        G+ +  +        
Sbjct: 63  QAMAFDGIIFQGQSLKIRRPHDYQPL 88

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 5e-12
 Identities = 9/85 (10%), Positives = 35/85 (41%), Gaps = 7/85 (8%)

Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETV-----MLMDQQTKRHRGFGFVTFENEEVV 304
           ++++VG +    + E +  +F+   ++          ++  Q  + + F F+ F + +  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 305 DHICEIHFHMIKNKKVECKKAQPKE 329
                    + + + ++ ++  P +
Sbjct: 62  TQAMAFDGIIFQGQSLKIRR--PHD 84

>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 = 60.8 bits (147), Expect = 1e-12
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 7/88 (7%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
               +  K ++V  +   TS E ++  F+             ++ K+ R + FV F N E
Sbjct: 2   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNRE 55

Query: 303 VVDH-ICEIHFHMIKNKKVECKKAQPKE 329
                +  ++  ++    +E   A+P +
Sbjct: 56  DAVEAMKALNGKVLDGSPIEVTLAKPVD 83

>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 = 50.4 bits (120), Expect = 6e-09
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 7/81 (8%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
            L+V  L   TS E + + F                 ++ R + F+ F+  E   + +K 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 222 VPIHTLDGKKIDPKHATPKNR 242
           +    LDG  I+   A P ++
Sbjct: 64  LNGKVLDGSPIEVTLAKPVDK 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 = 61.4 bits (148), Expect = 2e-12
 Identities = 9/94 (9%), Positives = 31/94 (32%), Gaps = 1/94 (1%)

Query: 156 GD-DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
           GD +       +  + +  +   + ++        + + +      +  G   + F   +
Sbjct: 2   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 215 TVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNR 248
              K  ++    L+G++      T ++  +I   
Sbjct: 62  DARKSERLHRKKLNGREAFVHVVTLEDMREIEKN 95

>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 = 61.4 bits (148), Expect = 2e-12
 Identities = 18/108 (16%), Positives = 39/108 (36%)

Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
           KS     RS           +++ GL ++  ++ + ++F     V D + +      ++ 
Sbjct: 1   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 60

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
           G GF+ F      +  L      +  + I     T K   +  +  +K
Sbjct: 61  GEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRK 108

>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 = 58.4 bits (140), Expect = 2e-11
 Identities = 18/108 (16%), Positives = 40/108 (37%)

Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
           P                 +++ G+  +   + V  +F +   VE+++ +      +  G 
Sbjct: 3   PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 62

Query: 294 GFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRV 341
           GFV F NE         H   + N+ ++      K  ++   ++ KR+
Sbjct: 63  GFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRL 110

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 11/77 (14%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           K+ V  +    S  +++  F++FG +++   +   ++ R  G   V FE +      + +
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 310 IHFHMIKNKKVECKKAQ 326
            +   +  + +  +   
Sbjct: 61  YNGVPLDGRPMNIQLVT 77

>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 = 2e-12
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KL V  L +  S   ++E F  FG +    +  D  + RS G   + F       K +K 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK- 59

Query: 223 PIHTLDGKKID 233
                +G  +D
Sbjct: 60  ---QYNGVPLD 67

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
            + V  + QD +  E+ A F   G +    ++ D +T    G+ FV F +E      I  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 310 IHFHMIKNKKVECKKAQP 327
           ++   ++NK+++   A+P
Sbjct: 64  LNGITVRNKRLKVSYARP 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 59.2 bits (143), Expect = 5e-12
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           ++  L V  L    +  +L   F   G +    IM+D  T  S G+ F+ F      ++ 
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 220 LKVPI-HTLDGKKIDPKHATP 239
           +KV    T+  K++   +A P
Sbjct: 61  IKVLNGITVRNKRLKVSYARP 81

>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 = 60.1 bits (145), Expect = 3e-12
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
           P      +A + V  LS  T    L+E F  FG+++ + + KD  T +S+GF FI+F   
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 214 ETVEKVLK-VPIHTLDGKKIDPKHATPKN 241
           E   + +  V     D   ++ + A P  
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKPST 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 4e-12
 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           NR    N T  I V  +S+DT   +++  F  FG +    +  D+ T + +GF F++F  
Sbjct: 2   NRRADDNAT--IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 59

Query: 301 EEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
            E     I  +      +  +  + A+P  
Sbjct: 60  REDAARAIAGVSGFGYDHLILNVEWAKPST 89

>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 = 59.7 bits (144), Expect = 4e-12
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 7/97 (7%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           S G   R  P G++    +++VG L     ++ + + F  +GA+ D+ +      +    
Sbjct: 1   SGGGVIRG-PAGNNDC--RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPP 54

Query: 205 FGFITFAEPETVEKVLKVPI-HTLDGKKIDPKHATPK 240
           F F+ F +P   E  +     +  DG ++  +     
Sbjct: 55  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 59.3 bits (143), Expect = 6e-12
 Identities = 14/88 (15%), Positives = 35/88 (39%), Gaps = 4/88 (4%)

Query: 242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
           R   GN   +I+VG +  D   ++++  F ++G + +  +   +       F FV FE+ 
Sbjct: 7   RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDP 63

Query: 302 EVVDH-ICEIHFHMIKNKKVECKKAQPK 328
              +  +     +     ++  +  +  
Sbjct: 64  RDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 59.3 bits (143), Expect = 4e-12
 Identities = 9/80 (11%), Positives = 27/80 (33%), Gaps = 4/80 (5%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
            +   P    + V  + +  S +++ ++F  +  +   + +K        G   + F   
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 214 ETVEKVLKVPIHTLDGKKID 233
           +     +      L+ + I 
Sbjct: 62  DEATAAVI----DLNDRPIG 77

>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 = 55.1 bits (132), Expect = 2e-10
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
            I V  +    S +E+  +F  +  +  +V L   +     G   V FE+ +     + +
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 310 IHFHMIKNKKVECKKA 325
           ++   I ++KV+    
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>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 = 59.3 bits (143), Expect = 5e-12
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
           K+++G +S   +A++++  F            +  Q     G+ FV + ++       E 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 311 --HFHMIKNKKVECKKAQPKE 329
                 +  K +E   +  K+
Sbjct: 57  LSGKVELHGKIMEVDYSVSKK 77

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 1e-11
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           KL++G LS   +++ LR+ FG         ++         G+ F+ + +     + ++ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIET 56

Query: 223 --PIHTLDGKKIDPKHATPK 240
                 L GK ++  ++  K
Sbjct: 57  LSGKVELHGKIMEVDYSVSK 76

>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 = 59.5 bits (143), Expect = 6e-12
 Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 1/93 (1%)

Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
           N P   N    + + G+    S EE+  +FS    V   + L      R  G  FV F +
Sbjct: 8   NSPDTAN-DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFAS 66

Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
           +E+ +   + H   I ++ +E  K+   E   +
Sbjct: 67  QEIAEKALKKHKERIGHRYIEIFKSSRAEVRTS 99

>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 = 59.4 bits (143), Expect = 6e-12
 Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           D      +F+  LS+ +  E L E    FG +  V ++  P T+ S+G  F  F   E  
Sbjct: 4   DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 63

Query: 217 EKVLKVPIH-------TLDGKKIDPKHATPKNR 242
           +K L             LDG+++    A  ++ 
Sbjct: 64  QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>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 = 53.7 bits (128), Expect = 7e-10
 Identities = 16/94 (17%), Positives = 36/94 (38%), Gaps = 7/94 (7%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           P      K +F+  +S D+  E +     QFG ++   +++   T+  +G  F  F  +E
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 303 VVD-------HICEIHFHMIKNKKVECKKAQPKE 329
                        E     +  ++++   A  ++
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 95

>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 = 59.0 bits (142), Expect = 9e-12
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 9/93 (9%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLI--------MKDPITQRSRGFGFI 208
           +D  ++ ++V GL+   + + L ++F   G V               D  T + +G   +
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 209 TFAEPETVEKVLKVPI-HTLDGKKIDPKHATPK 240
           ++ +P T +  ++        G K+    A  K
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 56.7 bits (136), Expect = 6e-11
 Identities = 16/100 (16%), Positives = 41/100 (41%), Gaps = 9/100 (9%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML--------MDQQTKRHRGFG 294
           P   +    I+V G++   + +++  +F Q G V+             +D++T + +G  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 295 FVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQA 333
            V++E+       +        +  K++   A+ K  + +
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 18/82 (21%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           ++T  + V  + Q+ + EE ++ F   G++E   ++ D+ T +  G+GFV + + +  + 
Sbjct: 1   SKTN-LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 307 -ICEIHFHMIKNKKVECKKAQP 327
            I  ++   ++ K ++   A+P
Sbjct: 60  AINTLNGLRLQTKTIKVSYARP 81

>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 = 55.9 bits (134), Expect = 7e-11
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            L V  L    + E+ R  FG  G +    +++D IT +S G+GF+ + +P+  EK +  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 223 PI-HTLDGKKIDPKHATP 239
                L  K I   +A P
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>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 = 58.5 bits (141), Expect = 1e-11
 Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 3/88 (3%)

Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
           P+        +F+  L     ++ L + F  FG +    ++ D     S+G+GF+ F   
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQ 58

Query: 214 ETVEKVLK-VPIHTLDGKKIDPKHATPK 240
           E  E+ ++ +    L+ +K+       +
Sbjct: 59  EAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 16/84 (19%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           +    IF+  + +    + +   FS FG +    ++ D+   +   +GFV FE +E  + 
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAER 63

Query: 307 -ICEIHFHMIKNKKVECKKAQPKE 329
            I +++  ++ ++KV   + + ++
Sbjct: 64  AIEKMNGMLLNDRKVFVGRFKSRK 87

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.9 bits (139), Expect = 1e-11
 Identities = 8/78 (10%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
            +++       +   ++        V  ++ L   +    R F ++   ++E   + + +
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 310 IHFHMIKNKKVECKKAQP 327
           ++   I+   +  K + P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>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 = 54.0 bits (129), Expect = 3e-10
 Identities = 11/79 (13%), Positives = 26/79 (32%), Gaps = 1/79 (1%)

Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
             L++       +   +R+       V   + +       SR F +I     E     ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 222 -VPIHTLDGKKIDPKHATP 239
            +    ++G  +  K + P
Sbjct: 62  KLNGLKIEGYTLVTKVSNP 80

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
            + + ++VG +S+D +   +   FSQ G  +   M+ +  +     + FV F        
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAA 63

Query: 307 -ICEIHFHMIKNKKVECKKAQPK 328
            +  ++   I  K+V+   A   
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTP 86

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 5e-11
 Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 3/89 (3%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           DD     L+VG LS   +   + + F   G      ++ +     +  + F+ F E    
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDA 61

Query: 217 EKVLK-VPIHTLDGKKIDPKHATPKNRPK 244
              L  +    + GK++    AT  +  K
Sbjct: 62  AAALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 58.1 bits (140), Expect = 2e-11
 Identities = 12/85 (14%), Positives = 32/85 (37%), Gaps = 4/85 (4%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
            + +++  +    +AEE+   F ++G + +  +         RG  +V +E+     +  
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAC 63

Query: 308 CEIHFHMIKNKKVECKKAQPKEAVQ 332
             +    + N+ +         A Q
Sbjct: 64  DHLSGFNVCNRYLVVLYYNANRAFQ 88

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 9e-11
 Identities = 14/117 (11%), Positives = 45/117 (38%), Gaps = 15/117 (12%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
             +  L++  L ++ ++E++ + FG +G +     ++   T  +RG  ++ + +    + 
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 219 VLK-VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG 274
               +    +  + +   +       +  +  KK            E++K    ++G
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKK-----------EEQLKLLKEKYG 107

>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 = 56.8 bits (136), Expect = 3e-11
 Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 2/76 (2%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
            + V  L    +  K+ +YF   G +  V +           F  I FA  +     +  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAAITK 59

Query: 223 PIHTLDGKKIDPKHAT 238
               +   +I   H T
Sbjct: 60  THKVVGQNEIIVSHLT 75

>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 = 51.4 bits (122), Expect = 2e-09
 Identities = 7/75 (9%), Positives = 21/75 (28%), Gaps = 2/75 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            + V  + +  +  +V  YF   G +    +    +      F  + F   +        
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAAITK 59

Query: 311 HFHMIKNKKVECKKA 325
              ++   ++     
Sbjct: 60  THKVVGQNEIIVSHL 74

>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 = 56.3 bits (135), Expect = 1e-10
 Identities = 14/103 (13%), Positives = 33/103 (32%), Gaps = 2/103 (1%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S  +    T   + + GL ++ +   +  +F     +   + +      R  G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEA 58

Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
            + FA  E     +      +  + ++    +       G  +
Sbjct: 59  DVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSS 101

>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 = 49.4 bits (117), Expect = 2e-08
 Identities = 11/84 (13%), Positives = 24/84 (28%), Gaps = 2/84 (2%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            + + G+    +  ++  +FS        V +      R  G   V F   E        
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNP--MRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 74

Query: 311 HFHMIKNKKVECKKAQPKEAVQAN 334
               ++++ VE           + 
Sbjct: 75  DKANMQHRYVELFLNSTAGTSGSG 98

>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 = 55.7 bits (133), Expect = 1e-10
 Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 4/93 (4%)

Query: 236 HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF 295
           H    +          +F+G ++ + S  E+K   S+     +  ++   +T  +R FG+
Sbjct: 3   HMVEGSEST---TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGY 58

Query: 296 VTFENEEVVDHICEIHFHMIKNKKVECKKAQPK 328
           V FE+ E ++   E+    +   +++ +K + +
Sbjct: 59  VDFESAEDLEKALELTGLKVFGNEIKLEKPKGR 91

>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 = 54.6 bits (130), Expect = 2e-10
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 2/92 (2%)

Query: 150 GRSTPTGDDP-TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
           G     G +  T   LF+G L+   S  +L+       A  D+ ++    T  +R FG++
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYV 59

Query: 209 TFAEPETVEKVLKVPIHTLDGKKIDPKHATPK 240
            F   E +EK L++    + G +I  +    +
Sbjct: 60  DFESAEDLEKALELTGLKVFGNEIKLEKPKGR 91

>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 = 55.8 bits (134), Expect = 1e-10
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 13/92 (14%)

Query: 157 DDPTSAK-------LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
           +DP ++K       L    LS+  + ++L+E F          I       +S+G  +I 
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIE 59

Query: 210 FAEPETVEKVLKVPI-HTLDGKKIDPKHATPK 240
           F      EK L+      +DG+ +   +   K
Sbjct: 60  FKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
            + +    +S + + +E+K  F          + +  Q  + +G  ++ F++E   +  +
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70

Query: 308 CEIHFHMIKNKKVECKKAQPK 328
            E     I  + V       K
Sbjct: 71  EEKQGAEIDGRSVSLYYTGEK 91

>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 = 55.1 bits (132), Expect = 1e-10
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
           + + +++ G   D + +++K +    G+V    M      K  +G  FV F++ E     
Sbjct: 5   KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-RRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 308 CEIHFHMIKNKKVECKKA 325
            E      K   +     
Sbjct: 64  VETPGQKYKETDLLILFK 81

>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 = 53.6 bits (128), Expect = 5e-10
 Identities = 12/81 (14%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +D  +  +++ G     + + ++E+    G V ++  M+  + +  +G  F+ F   E+ 
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI-QMRRTLHKAFKGSIFVVFDSIESA 60

Query: 217 EKVLKVPIHTLDGKKIDPKHA 237
           +K ++ P        +     
Sbjct: 61  KKFVETPGQKYKETDLLILFK 81

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 161 SAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIMKD-PITQRSRGFGFITFAEPETVEK 218
             ++ +  LS +   E  LRE F  FG++  + I         +    F+ F   ++ E+
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 219 VLKVPIHTLDGKKIDPKHATPK 240
            L++    L  ++I    A  K
Sbjct: 64  ALQMNRSLLGNREISVSLADKK 85

>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 = 54.8 bits (131), Expect = 2e-10
 Identities = 15/81 (18%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 250 KKIFVGGVSQDTSAEE-VKAYFSQFGKVEETVMLMDQ-QTKRHRGFGFVTFENEEVVDHI 307
           ++I +  +S +   E  ++  F  FG +E+  +   Q +   +    F+ FEN++  +  
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 308 CEIHFHMIKNKKVECKKAQPK 328
            +++  ++ N+++    A  K
Sbjct: 65  LQMNRSLLGNREISVSLADKK 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 7/82 (8%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           ++FVG +  D + EE++  F ++GK  E  +         +GFGF+  E   + +    E
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKVE 63

Query: 310 IHFHMIKNKKVECKKAQPKEAV 331
           +    ++ K++  + A    ++
Sbjct: 64  LDNMPLRGKQLRVRFACHSASL 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (127), Expect = 9e-10
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
           +LFVG L    + E++R+ F  +G   +V I KD        FGFI        E     
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 222 VPIHTLDGKKIDPKHATPK 240
           +    L GK++  + A   
Sbjct: 64  LDNMPLRGKQLRVRFACHS 82

>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 = 54.4 bits (130), Expect = 5e-10
 Identities = 17/88 (19%), Positives = 44/88 (50%), Gaps = 1/88 (1%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           P +    + +FVG +  + + E++K  FS+ G V    ++ D++T + +G+GF  ++++E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 303 VVDH-ICEIHFHMIKNKKVECKKAQPKE 329
                +  ++      + +    A  ++
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEK 89

>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 = 52.1 bits (124), Expect = 3e-09
 Identities = 20/99 (20%), Positives = 45/99 (45%), Gaps = 4/99 (4%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
           D +   +FVG + ++ + E+L++ F   G V    ++ D  T + +G+GF  + + ET  
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 218 KVLK-VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVG 255
             ++ +      G+ +   +A  +   +     K +  G
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNKE---ELKSLGTG 100

>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 = 54.0 bits (129), Expect = 6e-10
 Identities = 16/85 (18%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
           G   K +++  +S   +  ++ + F++F + +   +     T R RG  F+TF N+E+  
Sbjct: 15  GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 74

Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
             +  ++ + +  K +  +  + K+
Sbjct: 75  QALHLVNGYKLYGKILVIEFGKNKK 99

>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 = 53.6 bits (128), Expect = 7e-10
 Identities = 22/85 (25%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
            +P    L++  LS + +   L   F  F       I    +T R RG  FITF   E  
Sbjct: 15  GEPNK-VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 73

Query: 217 EKVLKVPI-HTLDGKKIDPKHATPK 240
            + L +   + L GK +  +    K
Sbjct: 74  WQALHLVNGYKLYGKILVIEFGKNK 98

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 6e-10
 Identities = 12/89 (13%), Positives = 39/89 (43%), Gaps = 2/89 (2%)

Query: 249 TKKIFVGGVSQDTSAEEVK-AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
              I++  +++    +E+K +  + F +  + + ++  ++ + RG  FV F+      + 
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 307 ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
           +  +      +K +  + A+    + A +
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 8e-10
 Identities = 12/83 (14%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 161 SAKLFVGGLSWQTSSEKLRE-YFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
           +  +++  L+ +   ++L++    +F     +L +    + + RG  F+ F E  +    
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 220 LK-VPIHTLDGKKIDPKHATPKN 241
           L+ +       K +  ++A   +
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDS 85

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 12/76 (15%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
            P +  ++ GG++   + + +R+ F  FG + ++ +  +        + F+ F+  E+  
Sbjct: 15  SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAA 68

Query: 218 KVLKVPIHTLDGKKID 233
             +     +++G  I+
Sbjct: 69  HAIV----SVNGTTIE 80

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 20/102 (19%), Positives = 44/102 (43%), Gaps = 11/102 (10%)

Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT 287
           + K++  +    ++ PK       ++ GG++   + + ++  FS FG++ E  +      
Sbjct: 1   NTKQLRFEDVVNQSSPK----NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF----- 51

Query: 288 KRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
              +G+ FV F   E   H I  ++   I+   V+C   +  
Sbjct: 52  -PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
              LFV  +  +   ++++E F  +G + ++ +  D  T  S+G+  + +   +      
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 221 K-VPIHTLDGKKIDPKHATPK 240
           + +    + G+ I       K
Sbjct: 67  EALNGAEIMGQTIQVDWCFVK 87

>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 = 50.5 bits (120), Expect = 7e-09
 Identities = 12/78 (15%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
           +FV  + ++   +E++  F  +G+++   + +D++T   +G+  V +E  +        +
Sbjct: 10  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 311 HFHMIKNKKVECKKAQPK 328
           +   I  + ++      K
Sbjct: 70  NGAEIMGQTIQVDWCFVK 87

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 7/83 (8%), Positives = 25/83 (30%), Gaps = 8/83 (9%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            + V G  Q ++   +   F+Q+        ++         +  + ++++         
Sbjct: 6   WVTVFGFPQASA-SYILLQFAQY------GNILKHVMSNTGNWMHIRYQSKLQARKALSK 58

Query: 311 HFHMIKNK-KVECKKAQPKEAVQ 332
              +      +  K    K  ++
Sbjct: 59  DGRIFGESIMIGVKPCIDKNVME 81

>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 = 49.2 bits (117), Expect = 1e-08
 Identities = 13/82 (15%), Positives = 23/82 (28%), Gaps = 8/82 (9%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
              + V G    ++S  L + F  +G +   ++           +  I +       K L
Sbjct: 4   DTWVTVFGFPQASASYILLQ-FAQYGNILKHVMSNT------GNWMHIRYQSKLQARKAL 56

Query: 221 KVPIHTLDGK-KIDPKHATPKN 241
                       I  K    KN
Sbjct: 57  SKDGRIFGESIMIGVKPCIDKN 78

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (118), Expect = 9e-09
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
           L++ GL   T+ + L +    +G +     + D  T + +G+GF+ F  P   +K     
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA---- 56

Query: 224 IHTLDGKKIDPKHA 237
           +  L    +  + A
Sbjct: 57  VTALKASGVQAQMA 70

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 49.1 bits (116), Expect = 7e-08
 Identities = 19/101 (18%), Positives = 46/101 (45%), Gaps = 1/101 (0%)

Query: 230 KKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR 289
           ++   +H  P       +  + + V  +       +++  F ++G +E   ++ D++T++
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQ 82

Query: 290 HRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
            RG+GFV F++       I  ++   I NK+++   A    
Sbjct: 83  SRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>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 = 45.3 bits (106), Expect = 1e-06
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           +      L V  +       +LR+ F  +G +  V I+ D  T++SRG+GF+ F    + 
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 217 EKVLKVPI-HTLDGKKIDPKHATPKN-RPKIGNRTK 250
           ++ +       +  K++    A   + RP I     
Sbjct: 98  QQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG 133

>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 = 47.5 bits (112), Expect = 7e-08
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 163 KLFVGGLSWQTSSE---KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
            +FV GLS + +     K  EYFG FG +  V+I        S+G     +      E  
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 220 LKVPIHTLDGKKIDPK 235
           L+  I  ++   +D +
Sbjct: 70  LRA-IQCVNNVVVDGR 84

>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 = 41.7 bits (97), Expect = 8e-06
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 251 KIFVGGVSQDTSAEEVKAYF---SQFGKVEETVMLMDQQTKRHRGFGFVTFEN----EEV 303
            +FV G+SQ  +  EV        +FGK+ + V+         +G     +      E+ 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 304 VDHICEIHFHMIKNKKVEC 322
           +  I  ++  ++  + ++ 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>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 = 47.2 bits (112), Expect = 1e-07
 Identities = 9/67 (13%), Positives = 26/67 (38%), Gaps = 5/67 (7%)

Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC 322
           E+++   S+FG++ +    +    +   G   V+F + E  D+    +       +++  
Sbjct: 34  EDLRVECSKFGQIRK----LLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 323 KKAQPKE 329
           +      
Sbjct: 90  QAWDGTT 96

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 5/73 (6%)

Query: 171 WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHT-LDG 229
                E LR     FG +  +L+          G   ++F +PE  +  ++        G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 230 KKIDPKHATPKNR 242
           ++I  +       
Sbjct: 85  RQITAQAWDGTTD 97

>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 = 46.9 bits (111), Expect = 2e-07
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++ V  L +  + + L + F  FG V  ++       + ++    + +A+P + +     
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVSAQHA--- 61

Query: 223 PIHTLDGKKI 232
              +LDG+ I
Sbjct: 62  -KLSLDGQNI 70

>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 = 39.6 bits (92), Expect = 6e-05
 Identities = 9/86 (10%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
           +   +I V  +    + + +   FS+FG V + +         ++    + + +     H
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQH 60

Query: 307 -ICEIHFHMI--KNKKVECKKAQPKE 329
               +    I      +    ++   
Sbjct: 61  AKLSLDGQNIYNACCTLRIDFSKLTS 86

>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 = 45.9 bits (108), Expect = 4e-07
 Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 9/105 (8%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S        S  + V GL        L E    FG +  V++M            
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QA 54

Query: 207 FITFAEPETVEKVLK---VPIHTLDGKKIDPKHATPKNRPKIGNR 248
            + F   ++ ++ +         + G++    ++T K   + GN 
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNS 99

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 7e-07
 Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 11/89 (12%)

Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
           SSG SG+    G    + +L+VGGL   TS   L   F  FG++  +  +K         
Sbjct: 2   SSGSSGKIGY-GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------ 54

Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
           F +I +   +  +         + G  + 
Sbjct: 55  FAYIQYESLDAAQAACA----KMRGFPLG 79

>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 = 35.8 bits (82), Expect = 0.001
 Identities = 11/83 (13%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
           T +++VGG+  +TS   +   F +F        +      +   F ++ +E+ +      
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRF------GSIRTIDHVKGDSFAYIQYESLDAAQAAC 70

Query: 308 CEIHFHMI--KNKKVECKKAQPK 328
            ++    +   ++++    A+  
Sbjct: 71  AKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 18/98 (18%), Positives = 31/98 (31%), Gaps = 14/98 (14%)

Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
           +  G    S  T     S  +  GGL    S  +L       G V  +L+  +       
Sbjct: 7   RHEGIETVSYAT----QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP----- 57

Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN 241
            + F  +   E  ++       TL+GK++         
Sbjct: 58  -YSFARYRTTEESKRA----YVTLNGKEVVDDLGQKIT 90

>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 = 42.9 bits (100), Expect = 4e-06
 Identities = 23/98 (23%), Positives = 33/98 (33%), Gaps = 8/98 (8%)

Query: 144 KSSGDSGR-STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
           K+SG   + +     DPT   L++  L      ++L      FG       +    +  S
Sbjct: 2   KASGVQAQMAKQQEQDPT--NLYISNLPLSMDEQELENMLKPFG-QVISTRILRDSSGTS 58

Query: 203 RGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPK 240
           RG GF      E  E V    I   +GK I        
Sbjct: 59  RGVGFARMESTEKCEAV----IGHFNGKFIKTPPGVSA 92

>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 = 42.5 bits (99), Expect = 7e-06
 Identities = 12/77 (15%), Positives = 24/77 (31%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
            +++  +      +E++     FG+V  T +L D                E+    I   
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 311 HFHMIKNKKVECKKAQP 327
           +   IK         +P
Sbjct: 80  NGKFIKTPPGVSAPTEP 96

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE-EVVDHI 307
           +  I V  + QD++ +EV      +               R++   FVT  N  +  + I
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 308 CEIHFHMIKNKKVECKKAQPK 328
              H +  + K +  +     
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTD 78

>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 = 39.7 bits (92), Expect = 4e-05
 Identities = 11/90 (12%), Positives = 30/90 (33%), Gaps = 8/90 (8%)

Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
              S+ + V  L   ++ +++ +    +        +K     R++   F+T    E  +
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQ 54

Query: 218 KVLKVPIHT-LDGKKIDPKHATPKNRPKIG 246
             +++       GK +  +          G
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPTDALLCSG 84

>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 = 41.7 bits (97), Expect = 1e-05
 Identities = 16/103 (15%), Positives = 31/103 (30%), Gaps = 8/103 (7%)

Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
           G SG S       +  ++ V GL    S + L+++                   +  G G
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMG 53

Query: 207 FITFAEPETVEKVLKVPIHT-LDGKKIDPKHATPKNRPKIGNR 248
            + +   E +E  L+    T     + +  +         G  
Sbjct: 54  MVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPS 96

>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 = 40.5 bits (94), Expect = 3e-05
 Identities = 10/88 (11%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
           P       ++ V G+    S +++K +  +          +     +  G G V +  +E
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGMVEYLRKE 61

Query: 303 VVDH-ICEIHFHMIKNKKVECKKAQPKE 329
            +++ + ++     ++ + E    +   
Sbjct: 62  DMEYALRKLDDTKFRSHEGETSYIRVYP 89

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 13/81 (16%), Positives = 30/81 (37%), Gaps = 9/81 (11%)

Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
              L+V G     +   LR  F  FG + D+ +             F+T+ + E+ ++ +
Sbjct: 5   GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAV 56

Query: 221 KVP-IHTLDGKKIDPKHATPK 240
                  ++  ++    A  +
Sbjct: 57  AELNGTQVESVQLKVNIARKQ 77

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 10/93 (10%), Positives = 25/93 (26%), Gaps = 12/93 (12%)

Query: 249 TKKIFVGGV-----SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
           +  +          S+  +  + ++ F  + K                    + F N   
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLS 58

Query: 304 VDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
                  +H      K+++   AQ      ++L
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLHIGSSHL 91

>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 = 38.2 bits (88), Expect = 2e-04
 Identities = 14/93 (15%), Positives = 22/93 (23%), Gaps = 12/93 (12%)

Query: 158 DPTSAKLFVGGL-----SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
              S+ L          S   +  K    F  +   T     K            I F+ 
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSN 55

Query: 213 PETVEKVLKVPIHT-LDGKKIDPKHATPKNRPK 244
           P +          T   GK++    A   +   
Sbjct: 56  PLSAADARLRLHKTEFLGKEMKLYFAQTLHIGS 88

>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 = 40.8 bits (95), Expect = 3e-05
 Identities = 12/92 (13%), Positives = 36/92 (39%), Gaps = 3/92 (3%)

Query: 233 DPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
           +P++++      + +    + +     +   E       ++G+VEE + + D       G
Sbjct: 12  NPQNSSQSADG-LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEE-MNVCDNLGDHLVG 69

Query: 293 FGFVTFENEEVVDH-ICEIHFHMIKNKKVECK 323
             +V F  EE  +  + +++      + +  +
Sbjct: 70  NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 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 = 40.1 bits (93), Expect = 3e-05
 Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
           P SA L +  +    S E L+  F   G V    +      Q+ R    I     E   +
Sbjct: 8   PPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQ 63

Query: 219 VLKVPIHT--LDGKKI 232
            L    +    +   +
Sbjct: 64  ALIDLHNHDLGENHHL 79

>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 = 37.4 bits (86), Expect = 3e-04
 Identities = 13/91 (14%), Positives = 28/91 (30%), Gaps = 6/91 (6%)

Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
           KN   I   +  + +  +    S E++K  FS  G V +      +  K       +   
Sbjct: 1   KNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA----LIQMG 56

Query: 300 NEEVVDHICEIH--FHMIKNKKVECKKAQPK 328
           + E             + +N  +    ++  
Sbjct: 57  SVEEAVQALIDLHNHDLGENHHLRVSFSKST 87

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 2e-04
 Identities = 16/96 (16%), Positives = 27/96 (28%), Gaps = 10/96 (10%)

Query: 157 DDPTSAKL-FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
           ++     L F G L  QT  E L   F   G +  +  ++          G I F E   
Sbjct: 6   EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAK 59

Query: 216 VEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
                       +   +  ++         G   K+
Sbjct: 60  EA---LGKAKDANNGNLQLRNKEVTWEVLEGEVEKE 92

>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 = 37.5 bits (86), Expect = 4e-04
 Identities = 11/82 (13%), Positives = 28/82 (34%), Gaps = 8/82 (9%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN--EEVVDH 306
               F G +   T  E++   FS  G+++    +           G + F+   +E +  
Sbjct: 11  CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGK 64

Query: 307 ICEIHFHMIKNKKVECKKAQPK 328
             + +   ++ +  E      +
Sbjct: 65  AKDANNGNLQLRNKEVTWEVLE 86

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 8/88 (9%), Positives = 24/88 (27%), Gaps = 10/88 (11%)

Query: 249 TKKIFVGGV-SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
            + + +           ++      FG +   ++L            F+     E     
Sbjct: 8   RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN------KINEAFIEMATTEDAQAA 61

Query: 308 CEI---HFHMIKNKKVECKKAQPKEAVQ 332
            +       ++  K V    +Q  + ++
Sbjct: 62  VDYYTTTPALVFGKPVRVHLSQKYKRIK 89

>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 = 36.9 bits (85), Expect = 5e-04
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 6/67 (8%)

Query: 169 LSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGF--ITFAEPETVEKVLKVPIHT 226
             ++   E +R+    +G V  + I +        G G   + F      +K     +  
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKA----MQG 77

Query: 227 LDGKKID 233
           L G+K  
Sbjct: 78  LTGRKFA 84

>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 = 36.0 bits (82), Expect = 8e-04
 Identities = 15/97 (15%), Positives = 28/97 (28%), Gaps = 21/97 (21%)

Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
           ++ V GL    S + L+++                      G G + F   E +      
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREA-------GDVCYADVYRDGTGVVEFVRKEDMTYA--- 51

Query: 223 PIHTLDGKKID----------PKHATPKNRPKIGNRT 249
            +  LD  K             K   P++     +R+
Sbjct: 52  -VRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 87

>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 = 34.5 bits (78), Expect = 0.003
 Identities = 11/81 (13%), Positives = 30/81 (37%), Gaps = 8/81 (9%)

Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
           ++ V G+    S +++K +  +          +        G G V F  +E + + + +
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREA-------GDVCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 310 IHFHMIKNKKVECKKAQPKEA 330
           +     ++ + E    + K  
Sbjct: 55  LDNTKFRSHEGETAYIRVKVD 75

>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 = 35.2 bits (80), Expect = 0.002
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 9/80 (11%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           + P +  LF+  L  +T+   L   F  F    +V ++ +          F+ F      
Sbjct: 4   EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIA-----FVEFTTELQS 58

Query: 217 EKVLKVPIHTLDGKKIDPKH 236
                     L G KI P H
Sbjct: 59  NA----AKEALQGFKITPTH 74

>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 = 35.2 bits (80), Expect = 0.002
 Identities = 10/84 (11%), Positives = 29/84 (34%), Gaps = 9/84 (10%)

Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD--- 305
           ++ + +  +  + +  EV A    F        + +    + +   F+    EE      
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATEEAAITMV 61

Query: 306 HICEIHFHMIKNKKVECKKAQPKE 329
           +        ++N+ +  + +  KE
Sbjct: 62  NYYSAVTPHLRNQPIYIQYSNHKE 85

>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 = 34.1 bits (77), Expect = 0.004
 Identities = 12/87 (13%), Positives = 29/87 (33%), Gaps = 9/87 (10%)

Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
           D   S  L +  L  + +  ++      FG       + + +  + +   F+  A  E  
Sbjct: 4   DGAPSRVLHIRKLPGEVTETEVIALGLPFG------KVTNILMLKGKNQAFLELATEEAA 57

Query: 217 EKVLKVPI---HTLDGKKIDPKHATPK 240
             ++         L  + I  +++  K
Sbjct: 58  ITMVNYYSAVTPHLRNQPIYIQYSNHK 84

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	398
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.85
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.85
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.85
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.82
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.8
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.78
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.77
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.76
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.76
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.76
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.76
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.75
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.73
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.73
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.71
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.71
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.71
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.71
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.7
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.7
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.69
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.69
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.69
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.68
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.67
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.67
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.66
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.66
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.65
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
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	99.61
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.6
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.52
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.51
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	99.47
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.46
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.45
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.41
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.41
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.38
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.37
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.3
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.93
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.45
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.45
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.38
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.27
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.12
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.9
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.86

>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=100.00  E-value=9.8e-36  Score=255.11  Aligned_cols=174  Identities=39%  Similarity=0.761  Sum_probs=158.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+++++++..++.++|||||+|.+.++|.+|++.++..++++.+.+.+...
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            45899999999999999999999999999999999999999999999999999999999999888888888877765544


Q ss_pred             CCC---CccCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeC
Q psy6490         240 KNR---PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIK  316 (398)
Q Consensus       240 ~~~---~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~  316 (398)
                      ...   .......++|||+|||..+|+++|+++|+.||.|..+.|+.|..++.++|||||+|.+.++|++|+++++..|+
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~  164 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN  164 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEET
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeEC
Confidence            332   23344567899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEecCchHHHhh
Q psy6490         317 NKKVECKKAQPKEAVQA  333 (398)
Q Consensus       317 g~~i~v~~a~~k~~~~~  333 (398)
                      |+.|+|+||.+|+++..
T Consensus       165 G~~i~V~~A~~k~e~~~  181 (183)
T d1u1qa_         165 GHNCEVRKALSKQEMAS  181 (183)
T ss_dssp             TEEEEEEECCCHHHHHH
T ss_pred             CEEEEEEecCCcccccc
Confidence            99999999999987754

>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=99.86  E-value=6.4e-22  Score=145.27  Aligned_cols=80  Identities=38%  Similarity=0.666  Sum_probs=76.3

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      +..++|||+|||+++|+++|+++|++||.|.+++|++|+.+|+++|||||+|.+.++|++|++++++.|+|+.|+|+.|.
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~   83 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999885

>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=99.86  E-value=8.6e-22  Score=146.08  Aligned_cols=82  Identities=15%  Similarity=0.309  Sum_probs=75.7

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++|+++|+++|+.||.|++|++++|+.+|+++|||||+|++.++|+.|+ .|||..|+|+.|+|+||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35678999999999999999999999999999999999999999999999999988777766 69999999999999999


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      .+|
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            876

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3.1e-22  Score=152.54  Aligned_cols=84  Identities=38%  Similarity=0.684  Sum_probs=79.5

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||+++|+++|+++|++||.|..+.|.+|+.++.++|||||+|.+.++|++|++++++.|+|+.|.|++|.
T Consensus        18 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHH
Q psy6490         327 PKEA  330 (398)
Q Consensus       327 ~k~~  330 (398)
                      ++++
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            8864

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.2e-21  Score=145.47  Aligned_cols=83  Identities=31%  Similarity=0.556  Sum_probs=76.6

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+|++||||||+|.+.++|+++++ ++..|+|+.|.|+++.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCC
Confidence            456789999999999999999999999999999999999999999999999999999988887 5668999999999998


Q ss_pred             chHH
Q psy6490         327 PKEA  330 (398)
Q Consensus       327 ~k~~  330 (398)
                      +++.
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8754

>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=99.86  E-value=1.2e-21  Score=149.41  Aligned_cols=85  Identities=20%  Similarity=0.375  Sum_probs=78.4

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||+++++++|+++|+.||.|.+++++.+..+|.+||||||+|.+.++|+.|+ +|||..|+|+.|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999988887766 69999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      +++.++
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            988653

>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=99.85  E-value=1e-21  Score=143.94  Aligned_cols=79  Identities=23%  Similarity=0.389  Sum_probs=74.3

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      +++|||+|||.++|+++|+++|++||.|++++|++|+.+|+++|||||+|.+.++|++|+ .|||..|+|+.|+|+|+++
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            467999999999999999999999999999999999999999999999999988887766 6999999999999999975

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=2.3e-22  Score=144.88  Aligned_cols=76  Identities=42%  Similarity=0.719  Sum_probs=73.4

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ++|||+|||+++|+++|+++|++||.|++++|++|+.+|++||||||+|.++++|+++++++++.|+||.|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999987

>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=8.6e-22  Score=149.63  Aligned_cols=83  Identities=16%  Similarity=0.354  Sum_probs=77.3

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|++|..+|++||||||+|.+.++|.+|++|||..|+|+.|+|+++.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCC
Confidence            35689999999999999999999999999999999999999999999999999888888889999999999999999876


Q ss_pred             hHH
Q psy6490         328 KEA  330 (398)
Q Consensus       328 k~~  330 (398)
                      +..
T Consensus        97 ~~n   99 (101)
T d2cq4a1          97 EKN   99 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3e-21  Score=141.42  Aligned_cols=78  Identities=21%  Similarity=0.438  Sum_probs=73.4

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      ++|||+|||.++++++|+++|++||.|.+|++++|..++.++|||||+|.+.++|+.++ +|||..|+|+.|+|+||+|
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            56999999999999999999999999999999999999999999999999988887766 6999999999999999976

>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=99.85  E-value=7.7e-22  Score=146.73  Aligned_cols=82  Identities=24%  Similarity=0.513  Sum_probs=76.2

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++|+.++.++|||||+|.+.++|++++ .+||..|+|+.|+|+|++
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            4578999999999999999999999999999999999999999999999999988777766 699999999999999998


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.4e-21  Score=145.65  Aligned_cols=83  Identities=20%  Similarity=0.376  Sum_probs=76.4

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|.|++|+.++.++|||||+|.+.++|++|+ .|||..|+|+.|+|+|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            45678999999999999999999999999999999999999999999999999977776665 69999999999999999


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      +++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.2e-21  Score=140.14  Aligned_cols=77  Identities=39%  Similarity=0.789  Sum_probs=74.3

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      .++|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.|++.+++++||+.|+||.|+|++|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.84  E-value=3.8e-21  Score=144.05  Aligned_cols=82  Identities=20%  Similarity=0.333  Sum_probs=76.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ..+++|||+|||.++|+++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|+.|+ .|||..|+|+.|+|+|+
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            45689999999999999999999999999999999999999999999999999988777766 69999999999999998


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.84  E-value=7.1e-22  Score=141.36  Aligned_cols=75  Identities=47%  Similarity=0.780  Sum_probs=72.2

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      +|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|+++++++++.|+|+.|+|++|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.84  E-value=2e-21  Score=145.62  Aligned_cols=83  Identities=30%  Similarity=0.458  Sum_probs=77.1

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++|+++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|++|+ .|||..|+|+.|+|+||
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            34578999999999999999999999999999999999999999999999999988887776 69999999999999999


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      +++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8764

>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=1.5e-21  Score=140.09  Aligned_cols=75  Identities=41%  Similarity=0.763  Sum_probs=72.0

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      +|||+|||+++||++|+++|++||.|.++.|.+|+.+++++|||||+|.+.++|++++++++..|+|+.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999764

>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=99.84  E-value=4.7e-21  Score=139.40  Aligned_cols=77  Identities=23%  Similarity=0.397  Sum_probs=72.7

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      +|||+|||.++|+++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|+.++ .|||..|+||.|+|.|++.
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~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            5999999999999999999999999999999999999999999999999988887777 6999999999999999853

>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=99.83  E-value=5.6e-21  Score=145.03  Aligned_cols=84  Identities=25%  Similarity=0.414  Sum_probs=77.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||+++++++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++++ .||+..|+|+.|+|.++
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            34667999999999999999999999999999999999999999999999999988877766 69999999999999999


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      ..+..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            98754

>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=99.83  E-value=9e-21  Score=144.80  Aligned_cols=83  Identities=33%  Similarity=0.617  Sum_probs=75.9

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|++|++..+..|+||.|+|+|+.
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~   87 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAY   87 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEEST
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcC
Confidence            34567999999999999999999999999999999999999999999999999999998888765668999999999998


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      .+.
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
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=99.83  E-value=3.8e-21  Score=147.47  Aligned_cols=86  Identities=19%  Similarity=0.444  Sum_probs=78.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|+.|+ +|||..|+|+.|+|+|+.
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            4568999999999999999999999999999999999999999999999999988887766 689999999999999998


Q ss_pred             chHHHhh
Q psy6490         327 PKEAVQA  333 (398)
Q Consensus       327 ~k~~~~~  333 (398)
                      ++..+..
T Consensus        87 ~~~~~~~   93 (104)
T d1p1ta_          87 SEKNKEE   93 (104)
T ss_dssp             CTTHHHH
T ss_pred             CCCCccc
Confidence            8765554

>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=99.83  E-value=8.8e-21  Score=142.01  Aligned_cols=85  Identities=31%  Similarity=0.502  Sum_probs=79.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ....++|||+|||.++|+++|+++|++||.|.++++++|+.+|.++|||||+|.+.++|++|++ +++..++|+.|.|++
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3356899999999999999999999999999999999999999999999999999999999997 899999999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +..+.+
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            987654

>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=99.83  E-value=3.8e-21  Score=141.47  Aligned_cols=79  Identities=22%  Similarity=0.441  Sum_probs=73.6

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      .+|||+|||.++|+++|+++|++||.|++|+|++|+.+|.++|||||+|.+.++|..++ .|||..|+|+.|+|+|+.+.
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            46999999999999999999999999999999999999999999999999988777666 59999999999999999754

>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=99.83  E-value=9.4e-21  Score=153.27  Aligned_cols=84  Identities=19%  Similarity=0.433  Sum_probs=77.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||+++|+++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|+.++ .|||..|+||.|+|+|+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999988887766 58999999999999999


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      ..+..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.83  E-value=6.4e-21  Score=139.82  Aligned_cols=80  Identities=45%  Similarity=0.847  Sum_probs=75.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ...++|||+|||.++|+++|+++|++||.|.+++|++|+.+|+++|||||+|.+.++|++|+++++..|+|+.|.|+.+.
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~   83 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999987764

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.83  E-value=5.8e-21  Score=140.88  Aligned_cols=81  Identities=16%  Similarity=0.361  Sum_probs=70.7

Q ss_pred             cccceeecCCCCCCC-HHHHHHHHhhcCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         248 RTKKIFVGGVSQDTS-AEEVKAYFSQFGKVEETVMLMD-QQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       248 ~~~~l~V~nLp~~~t-ee~L~~~F~~~G~i~~v~i~~~-~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ..++|||+|||.+++ +++|+++|++||.|++|+|.++ ..+++++|||||+|.+.++|++|++||+..|+|+.|+|+|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            357899999999986 5569999999999999998764 56899999999999999999888899999999999999999


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      ++|
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>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=99.83  E-value=2.7e-20  Score=136.43  Aligned_cols=76  Identities=25%  Similarity=0.440  Sum_probs=71.1

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      .+.++|||+|||.++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|+ .|||..|+||.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45688999999999999999999999999999999999999999999999999988887766 69999999999987

>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=99.82  E-value=5.3e-21  Score=137.54  Aligned_cols=75  Identities=64%  Similarity=1.185  Sum_probs=72.4

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      +|||+|||+++||++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|++++++||+.|+||.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999986

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.82  E-value=1.1e-20  Score=138.01  Aligned_cols=78  Identities=10%  Similarity=0.204  Sum_probs=66.5

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      ++|||+|||.++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|+ .|||..|+|+.|+|++++|
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            68999999999999999999999999999999988889999999999999988777766 6999999999999999976

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.6e-20  Score=138.12  Aligned_cols=78  Identities=24%  Similarity=0.479  Sum_probs=71.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC--EEEEEEe
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN--KKVECKK  324 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v~~  324 (398)
                      ..++|||+|||.++|+++|+++|++||.|++++|++|+.+|.++|||||+|.+.++|++++ .|||..++|  ++|+|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            4567999999999999999999999999999999999999999999999999988887766 699999998  4599998


Q ss_pred             c
Q psy6490         325 A  325 (398)
Q Consensus       325 a  325 (398)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.82  E-value=5.3e-21  Score=142.60  Aligned_cols=83  Identities=33%  Similarity=0.621  Sum_probs=76.4

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||+++|+++|+++|+.||.|.++.++++..++.++|||||+|.+.++|+.++ .|||..|+|+.|+|+|+.
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            4567999999999999999999999999999999999999999999999999988887765 799999999999999998


Q ss_pred             chHH
Q psy6490         327 PKEA  330 (398)
Q Consensus       327 ~k~~  330 (398)
                      ++.+
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.82  E-value=1.2e-20  Score=141.61  Aligned_cols=83  Identities=24%  Similarity=0.431  Sum_probs=74.3

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHH-HH-CCceeCCEEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGFGFVTFENEEVVDHIC-EI-HFHMIKNKKVECK  323 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~-~~~~~kg~afV~F~~~eaa~a~~-~l-~~~~i~g~~i~v~  323 (398)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+ .| |+..|+|+.|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            456789999999999999999999999999999998875 47899999999999987776665 57 8999999999999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      ||..+.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998764

>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=99.82  E-value=2.6e-20  Score=142.23  Aligned_cols=87  Identities=37%  Similarity=0.693  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      .+...++|||+|||.++++++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|++|++..+..|+|++|.|++
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~   85 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNL   85 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEE
Confidence            33466889999999999999999999999999999999999999999999999999999999999655689999999988


Q ss_pred             CCCCCCC
Q psy6490         237 ATPKNRP  243 (398)
Q Consensus       237 ~~~~~~~  243 (398)
                      +..+..+
T Consensus        86 a~~~~~p   92 (103)
T d2cqda1          86 AYLGAKP   92 (103)
T ss_dssp             STTTCCC
T ss_pred             cCCCCCC
Confidence            8765443

>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=99.82  E-value=1.4e-20  Score=134.92  Aligned_cols=75  Identities=55%  Similarity=1.010  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +|||+|||+++|+++|+++|++||.|.++++.+|+.+++++|||||+|.+.++|++||++++..|+|+.|.|+.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            489999999999999999999999999999999999999999999999999999999999999999999988754

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1e-20  Score=138.81  Aligned_cols=79  Identities=22%  Similarity=0.431  Sum_probs=72.4

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCchH
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEET-VMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPKE  329 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v-~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k~  329 (398)
                      |||+|||+++|+++|+++|++||.|.++ ++++|..+|+++|||||+|.+.++|+.|+ +|||..|+|+.|+|+|+.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998664 78899999999999999999988887776 599999999999999998775


Q ss_pred             H
Q psy6490         330 A  330 (398)
Q Consensus       330 ~  330 (398)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.82  E-value=3.2e-20  Score=134.18  Aligned_cols=76  Identities=16%  Similarity=0.288  Sum_probs=70.2

Q ss_pred             ceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       251 ~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      +|||+|||+++++++|+++|++||.|++++|.+++ +++++|||||+|.+.++|+.|+ .|||..++|+.|+|+++.+
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            59999999999999999999999999999999985 8999999999999988776665 6999999999999999863

>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=99.82  E-value=2.3e-20  Score=138.50  Aligned_cols=82  Identities=41%  Similarity=0.666  Sum_probs=76.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      .+++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|++||+. ...|+|+.|.|+++..
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~-~~~l~Gr~i~v~~a~~   85 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKLPNS   85 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEECCCT
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc-CCccCCEEeEEEeCCC
Confidence            668999999999999999999999999999999999999999999999999999999999984 4579999999999877


Q ss_pred             CCC
Q psy6490         240 KNR  242 (398)
Q Consensus       240 ~~~  242 (398)
                      +..
T Consensus        86 k~~   88 (90)
T d2cqga1          86 KQS   88 (90)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            554

>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=99.82  E-value=2.4e-20  Score=137.27  Aligned_cols=78  Identities=17%  Similarity=0.419  Sum_probs=71.8

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC--EEEEEEe
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN--KKVECKK  324 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v~~  324 (398)
                      ..++|||+|||.++++++|+++|++||.|.++++++|+.+++++|||||+|.+.++|++|+ .|||..+.|  +.|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            4567999999999999999999999999999999999999999999999999988777666 699999977  8899999


Q ss_pred             c
Q psy6490         325 A  325 (398)
Q Consensus       325 a  325 (398)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.82  E-value=9.4e-21  Score=138.66  Aligned_cols=79  Identities=24%  Similarity=0.385  Sum_probs=75.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      +++|||+|||.++|+++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.++.+
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            4689999999999999999999999999999999999999999999999999999999997 899999999999998864

>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=99.81  E-value=5.1e-21  Score=137.76  Aligned_cols=76  Identities=61%  Similarity=1.088  Sum_probs=72.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ++|||+|||.++|+++|+++|++||.|.++++++|+.+|++||||||+|.+.++|++|++++++.++|+.|.|+.+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999988764

>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=99.81  E-value=4.4e-20  Score=137.37  Aligned_cols=82  Identities=20%  Similarity=0.337  Sum_probs=73.1

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++|+++|+++|+.||.|++|+|++|..++  +|||||+|.+.++|+.|+ .+||..|.|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456789999999999999999999999999999999986554  899999999988887766 69999999999999999


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      +++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87643

>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=99.81  E-value=1.8e-20  Score=139.50  Aligned_cols=83  Identities=29%  Similarity=0.462  Sum_probs=78.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++++++|+++|++||.|.+|++++|+.+|.++|||||+|.+.++|++|++ +++..++|++|.|.++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            367899999999999999999999999999999999999999999999999999999999998 8999999999999998


Q ss_pred             CCCC
Q psy6490         238 TPKN  241 (398)
Q Consensus       238 ~~~~  241 (398)
                      .++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            7653

>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=99.81  E-value=3e-20  Score=141.54  Aligned_cols=84  Identities=24%  Similarity=0.419  Sum_probs=79.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++++++|+++|+.||.|.+++++.++.+|.++|||||+|.+.++|++||+ +++..|+|+.|.|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999999999999999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      .++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87654

>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=99.81  E-value=1.6e-20  Score=143.03  Aligned_cols=83  Identities=41%  Similarity=0.859  Sum_probs=78.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      ..++|||+|||+++|+++|+++|++||.|.++.|.+|+.++.++|||||+|.+.++|.+|+++++..|+|+.|.|+++.+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcc
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CCC
Q psy6490         240 KNR  242 (398)
Q Consensus       240 ~~~  242 (398)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=4e-20  Score=136.21  Aligned_cols=77  Identities=21%  Similarity=0.446  Sum_probs=70.0

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTK---RHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~---~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      |||+|||.++|+++|+++|++||.|.+|+|++++.++   .+||||||+|++.++|++++ .|||..|+|+.|+|+|+..
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            7999999999999999999999999999999987665   47999999999988887766 6899999999999999865


Q ss_pred             h
Q psy6490         328 K  328 (398)
Q Consensus       328 k  328 (398)
                      +
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.81  E-value=2.2e-20  Score=138.36  Aligned_cols=81  Identities=16%  Similarity=0.277  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +.++|||+|||.++|+++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.++|++|++ +++..++|+.|.|+++.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            67899999999999999999999999999999999999999999999999999999999997 89999999999999886


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      .+
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            54

>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=99.81  E-value=1.6e-20  Score=134.26  Aligned_cols=75  Identities=47%  Similarity=0.710  Sum_probs=71.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +|||+|||+++|+++|+++|++||.|.+|++++|+.+++++|||||+|.+.++|++||+.+++.++|+.|.|+.+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999998888999999887653

>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=99.81  E-value=3.1e-20  Score=136.54  Aligned_cols=81  Identities=23%  Similarity=0.448  Sum_probs=76.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      .+|||+|||.++|+++|+++|++||+|.+|++++|+.+|+++|||||+|.+.++|.+|++ +++..++|+.|.|.++...
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            479999999999999999999999999999999999999999999999999999999998 8999999999999999765


Q ss_pred             CC
Q psy6490         241 NR  242 (398)
Q Consensus       241 ~~  242 (398)
                      .+
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.81  E-value=1.3e-19  Score=135.58  Aligned_cols=82  Identities=26%  Similarity=0.551  Sum_probs=73.2

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||+++++++|+++|+.||.|++|+++++.  +.++|||||+|.+.++|++|+ .||+..|+|+.|+|+|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3456789999999999999999999999999999999885  346999999999988777766 6999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      |++|.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98764

>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=99.81  E-value=5.8e-21  Score=142.22  Aligned_cols=82  Identities=20%  Similarity=0.350  Sum_probs=74.7

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ....++|||+|||+++|+++|+++|+.||.|.+++|+.+ .+|+++|||||+|.+.+++++|++|||..|+|+.|+|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            345668999999999999999999999999999888655 6899999999999999998888899999999999999999


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      +.|
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            864

>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=99.81  E-value=6.1e-20  Score=139.23  Aligned_cols=83  Identities=30%  Similarity=0.539  Sum_probs=78.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||+++++++|+++|++||.|.+|++++|+.+++++|||||+|.+.++|++||+ +++..|+|+.|.|.++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            56789999999999999999999999999999999999999999999999999999999997 89999999999999988


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      .+..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            7654

>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=99.80  E-value=4.1e-20  Score=134.34  Aligned_cols=76  Identities=26%  Similarity=0.516  Sum_probs=73.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +|||+|||.++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|.+|++ +++..++|++|+|.++.
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            69999999999999999999999999999999999999999999999999999999997 89999999999998875

>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=99.80  E-value=4e-20  Score=135.27  Aligned_cols=79  Identities=29%  Similarity=0.541  Sum_probs=75.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      .++|||+|||.++++++|+++|++||.|.+|+++++..++.++|||||+|.+.++|++|++ +++..++|+.|.|.++.+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            3679999999999999999999999999999999999999999999999999999999997 899999999999998864

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=8.4e-20  Score=134.09  Aligned_cols=78  Identities=18%  Similarity=0.307  Sum_probs=72.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++.++ .++++||||||+|.+.++|.+++++++..++|+.|+|+|..
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 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999999877 58999999999999999999999999999999999999863

>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=99.80  E-value=5.4e-20  Score=137.63  Aligned_cols=81  Identities=23%  Similarity=0.440  Sum_probs=77.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++|+++|+++|++||.|.+|++++++.++.++|||||+|.+.++|.+|++ +++..++|+.|.|.++.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            67899999999999999999999999999999999999999999999999999999999997 89999999999999876


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.80  E-value=6.6e-20  Score=134.90  Aligned_cols=79  Identities=22%  Similarity=0.483  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCC--cccCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDG--KKIDPK  235 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g--~~l~v~  235 (398)
                      ...++|||+|||.++++++|+++|++||.|.++++++|+.+|+++|||||+|.+.++|.+|++ +++..+.|  ++|.|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            366789999999999999999999999999999999999999999999999999999999998 88888876  778876


Q ss_pred             CC
Q psy6490         236 HA  237 (398)
Q Consensus       236 ~~  237 (398)
                      ++
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

>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=99.80  E-value=4e-20  Score=137.30  Aligned_cols=80  Identities=20%  Similarity=0.470  Sum_probs=72.6

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCc
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..+|||+|||.++|+++|+++|+.||.|.+++|+.+.  +.++|||||+|++.++|++|+ +|||..|+|+.|+|.++++
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 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999999985  347899999999988887777 6999999999999999998


Q ss_pred             hHH
Q psy6490         328 KEA  330 (398)
Q Consensus       328 k~~  330 (398)
                      +.+
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            754

>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=99.80  E-value=1.4e-20  Score=139.79  Aligned_cols=82  Identities=32%  Similarity=0.481  Sum_probs=77.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+|++++|+.+|.++|||||+|.+.++|++|++ +++..++|+.|.|.++.
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            56899999999999999999999999999999999999999999999999999999999997 89999999999999987


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=5.5e-20  Score=140.91  Aligned_cols=83  Identities=18%  Similarity=0.414  Sum_probs=74.4

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~-~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      .+.++|||+|||+++|+++|+++|+.|| |.+++++++. .+++++|||||+|.+.++|+++++||+..|+||.|+|+|+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4568999999999999999999999999 6777777765 4688999999999999999999999999999999999999


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T d1wi8a_          92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.80  E-value=8.2e-20  Score=138.46  Aligned_cols=84  Identities=17%  Similarity=0.331  Sum_probs=75.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-H------CCceeCCE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I------HFHMIKNK  318 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l------~~~~i~g~  318 (398)
                      ....++|||+|||+++|+++|+++|++||.|.+++++.+..++.++|||||+|.+.++|+++++ +      +|..|+||
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456789999999999999999999999999999999999999999999999999888877764 4      47889999


Q ss_pred             EEEEEecCchH
Q psy6490         319 KVECKKAQPKE  329 (398)
Q Consensus       319 ~i~v~~a~~k~  329 (398)
                      .|+|.|+.+|+
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998865

>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=99.80  E-value=2e-20  Score=141.99  Aligned_cols=79  Identities=24%  Similarity=0.407  Sum_probs=75.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      +.++|||+|||.++++++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.++|.+|+++++..|+|+.|.|+++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            4689999999999999999999999999999999999999999999999999999999999999999999999987653

>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=99.80  E-value=5.5e-20  Score=134.74  Aligned_cols=76  Identities=34%  Similarity=0.522  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      .++++|||+|||.++|+++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++ +++..++|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            367899999999999999999999999999999999999999999999999999999999997 8999999998865

>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=99.79  E-value=9e-20  Score=132.31  Aligned_cols=77  Identities=34%  Similarity=0.684  Sum_probs=73.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      .++|||+|||.++|+++|+++|++||.|..+++..++.++.++|||||+|.+.+++.+|+++++..|+|+.|.|+.+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.79  E-value=2.8e-19  Score=144.45  Aligned_cols=84  Identities=21%  Similarity=0.391  Sum_probs=78.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ...++|||+|||.++|+++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|.+||+ +++..|+|++|.|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            356799999999999999999999999999999999999999999999999999999999998 8999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      ..+..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.79  E-value=1.1e-19  Score=139.05  Aligned_cols=86  Identities=22%  Similarity=0.276  Sum_probs=78.6

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      .....+|||+|||+++|++||+++|+.||.|..++++.+..+++++|||||+|.++++|++++++|+..|+||.|+|.++
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            44556799999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             CchHHH
Q psy6490         326 QPKEAV  331 (398)
Q Consensus       326 ~~k~~~  331 (398)
                      ..++.+
T Consensus        92 ~~~~~~   97 (104)
T d1wg5a_          92 SRAEVR   97 (104)
T ss_dssp             CTTTSC
T ss_pred             CHHHhc
Confidence            877543

>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=99.79  E-value=1.7e-19  Score=135.16  Aligned_cols=83  Identities=27%  Similarity=0.490  Sum_probs=76.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCC-CCCCcccEEEEEEcChHhHHHHHh-C-CCcccCCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGFGFITFAEPETVEKVLK-V-PIHTLDGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~e~a~~al~-~-~~~~~~g~~l~v~~  236 (398)
                      .+++|||+|||.++++++|+++|+.||.|.+|+++++. .+|+++|||||+|.+.++|.+|++ + ++..++|++|.|.+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            66889999999999999999999999999999999875 478999999999999999999998 5 88899999999999


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +.....
T Consensus        87 A~~~~~   92 (94)
T d2cpha1          87 ADSEVT   92 (94)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            976653

>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=99.79  E-value=1.6e-19  Score=132.74  Aligned_cols=77  Identities=30%  Similarity=0.504  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcc--cCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKK--IDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~--l~v~~  236 (398)
                      .+++|||+|||.++|+++|+++|++||.|.++++++|+.+|.++|||||+|.+.++|++|++ +|+..+.|+.  |.|++
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999997 8999998854  66554

>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=99.78  E-value=1.5e-19  Score=138.11  Aligned_cols=87  Identities=10%  Similarity=0.151  Sum_probs=77.9

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ....+|||+|||+++|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++|+++|+..|+||.|.|.++.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            34567999999999999999999999999987666677689999999999999999999999999999999999999998


Q ss_pred             chHHHhh
Q psy6490         327 PKEAVQA  333 (398)
Q Consensus       327 ~k~~~~~  333 (398)
                      .++....
T Consensus        86 ~~~~~~~   92 (103)
T d2cpya1          86 LEDMREI   92 (103)
T ss_dssp             HHHHHHH
T ss_pred             HHHhhhh
Confidence            7766554

>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=99.78  E-value=2.3e-19  Score=136.72  Aligned_cols=84  Identities=18%  Similarity=0.338  Sum_probs=74.0

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE--------ETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~--------~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.        .+.+.++..+++++|||||+|.+.++|.+|+ .|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            44577999999999999999999999999874        5667788888999999999999987776655 69999999


Q ss_pred             CEEEEEEecCchH
Q psy6490         317 NKKVECKKAQPKE  329 (398)
Q Consensus       317 g~~i~v~~a~~k~  329 (398)
                      ||.|+|+|++++.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998764

>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=99.78  E-value=4.6e-20  Score=140.88  Aligned_cols=86  Identities=19%  Similarity=0.290  Sum_probs=78.0

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ..++++|||+|||.++++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|+.|+ .|||..|+|+.|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345789999999999999999999999999999999998889999999999999988877766 6899999999999999


Q ss_pred             cCchHHH
Q psy6490         325 AQPKEAV  331 (398)
Q Consensus       325 a~~k~~~  331 (398)
                      +++++++
T Consensus        95 ak~k~~r  101 (102)
T d2cpxa1          95 GKNKKQR  101 (102)
T ss_dssp             CCCCSCC
T ss_pred             CCCcccC
Confidence            9987643

>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=99.78  E-value=4.4e-19  Score=126.83  Aligned_cols=74  Identities=9%  Similarity=0.169  Sum_probs=68.3

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      ++|||+|||+++++++|+++|+.||.|.+|++.+++..  .+|||||+|+++++|++|+++|++.|+|+.|.|+.+
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--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999998643  467999999999999999999999999999999875

>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=99.77  E-value=1.4e-19  Score=134.80  Aligned_cols=83  Identities=36%  Similarity=0.695  Sum_probs=77.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +.++|||+|||.++++++|+++|+.||.|.++.++++..++.++|||||+|.+.++|++|++ +++..|+|+.|.|+++.
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            66889999999999999999999999999999999999999999999999999999999997 89999999999999886


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      .+..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.77  E-value=1.9e-19  Score=137.84  Aligned_cols=81  Identities=21%  Similarity=0.511  Sum_probs=76.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +.++|||+|||.++|+++|+++|+.||+|.+|++++++.+|+++|||||+|.+.++|++|++ +++..|+|+.|.|+++.
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            45789999999999999999999999999999999999999999999999999999999997 89999999999999876


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.1e-19  Score=136.67  Aligned_cols=80  Identities=14%  Similarity=0.274  Sum_probs=71.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      +.+++|||+|||.++|+++|+++|++||.|++|++..+   +.++|||||+|.+.++|..|+ .|||..|+|+.|+|.|+
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            34678999999999999999999999999999998754   567999999999988776666 79999999999999998


Q ss_pred             CchH
Q psy6490         326 QPKE  329 (398)
Q Consensus       326 ~~k~  329 (398)
                      ..+.
T Consensus        82 ~~~~   85 (114)
T d2f9da1          82 NANR   85 (114)
T ss_dssp             CHHH
T ss_pred             CCCc
Confidence            7643

>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=99.77  E-value=3.7e-19  Score=132.28  Aligned_cols=82  Identities=20%  Similarity=0.348  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      +.+.++|||+|||.++|+++|+++|+.||.|.+|++++++.++  +|||||+|.+.++|.+|++ +++..+.|+.|+|.+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4467899999999999999999999999999999999987554  8899999999999999998 899999999999999


Q ss_pred             CCCCC
Q psy6490         237 ATPKN  241 (398)
Q Consensus       237 ~~~~~  241 (398)
                      +.+..
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            87654

>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=99.77  E-value=7.2e-19  Score=132.10  Aligned_cols=75  Identities=21%  Similarity=0.499  Sum_probs=68.2

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++++++|+++|++||.|++|+|++|      ||||||+|++.++|++|+ .|||..|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3568999999999999999999999999999999876      789999999987776665 799999999999999997


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      ++
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.77  E-value=3.7e-19  Score=130.89  Aligned_cols=78  Identities=33%  Similarity=0.598  Sum_probs=71.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCC---CcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ---RSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       164 l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~---~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      |||+|||.++|+++|+++|++||.|.++++++++.++   .++|||||+|.+.++|.+|++ +++..++|+.|.|+++..
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            8999999999999999999999999999999887665   479999999999999999997 899999999999999865


Q ss_pred             CC
Q psy6490         240 KN  241 (398)
Q Consensus       240 ~~  241 (398)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.77  E-value=9.6e-19  Score=130.78  Aligned_cols=84  Identities=29%  Similarity=0.557  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      .....++|||+|||.++++++|+++|+.||.|.+|+++.++.  .++|||||+|.+.++|++|++ +++..++|++|.|+
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 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            334678999999999999999999999999999999999863  379999999999999999997 89999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++.++..
T Consensus        85 ~A~~r~~   91 (93)
T d2cq3a1          85 NATARVM   91 (93)
T ss_dssp             ECCSSCC
T ss_pred             ecCcCCC
Confidence            9987643

>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=99.76  E-value=2.1e-19  Score=129.01  Aligned_cols=75  Identities=45%  Similarity=0.812  Sum_probs=71.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +|||+|||.++|+++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|++|+++++..|+|+.|.|+++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.76  E-value=1.8e-19  Score=131.34  Aligned_cols=78  Identities=14%  Similarity=0.241  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      ++|||+|||.++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|.+|++ +++..++|++|.|+++.+
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            699999999999999999999999999999998888899999999999999999999997 899999999999988764

>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=99.76  E-value=1.6e-18  Score=132.43  Aligned_cols=86  Identities=22%  Similarity=0.325  Sum_probs=77.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      +.....+|||+|||+++|+++|+++|+.||.|..+.++.+..+++++|||||+|.+.++|++|+++++..|+||.|.|..
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEE
Confidence            34466789999999999999999999999999887777877899999999999999999999999999999999999988


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +.....
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            876544

>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=99.76  E-value=2.9e-19  Score=130.88  Aligned_cols=79  Identities=28%  Similarity=0.468  Sum_probs=73.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCEEE-EEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCCC
Q psy6490         164 LFVGGLSWQTSSEKLREYFGMFGAVTD-VLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKN  241 (398)
Q Consensus       164 l~v~nLp~~~t~~~L~~~f~~~G~i~~-~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~~  241 (398)
                      |||+|||.++|+++|+++|++||.|.+ +++++++.+|+++|||||+|.+.++|++|++ +++..++|++|.|.++.++.
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            899999999999999999999999866 4788999999999999999999999999997 89999999999999987654


Q ss_pred             C
Q psy6490         242 R  242 (398)
Q Consensus       242 ~  242 (398)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.76  E-value=2.3e-19  Score=132.14  Aligned_cols=81  Identities=21%  Similarity=0.318  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHHHhcCCCEEEEEEeeC-CCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTS-SEKLREYFGMFGAVTDVLIMKD-PITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t-~~~L~~~f~~~G~i~~~~~~~~-~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      +.++|||+|||.+++ +++|+++|++||.|.+|++..+ +.+++++|||||+|.+.++|++|+++++..++|+.|.|.++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            578999999999976 5669999999999999998764 56889999999999999999999999999999999999988


Q ss_pred             CCC
Q psy6490         238 TPK  240 (398)
Q Consensus       238 ~~~  240 (398)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.76  E-value=5.3e-19  Score=134.37  Aligned_cols=80  Identities=20%  Similarity=0.392  Sum_probs=71.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.++++..+ .++.++|||||+|.+.++|++|+ +|||..|+||.+.|.++.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            4578999999999999999999999999999999888 58899999999999988776665 699999999999998876


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      |.
T Consensus        96 Pl   97 (101)
T d1x5oa1          96 PL   97 (101)
T ss_dssp             CB
T ss_pred             Cc
Confidence            53

>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=99.76  E-value=3.6e-19  Score=128.54  Aligned_cols=75  Identities=27%  Similarity=0.406  Sum_probs=71.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       163 ~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +|||+|||.++++++|+++|++||.|.++++..++ +|+++|||||+|.+.++|.+|++ +++..++|+.|.|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999986 89999999999999999999998 89999999999987654

>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=99.76  E-value=2.6e-19  Score=136.34  Aligned_cols=83  Identities=12%  Similarity=0.118  Sum_probs=73.5

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ......+|||+|||+++|++||+++|+.|| |.+|.++++ .++.++|||||+|++.++|++|+++|++.|+||.|+|.|
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344567899999999999999999999998 456888877 468999999999999999988899999999999999999


Q ss_pred             cCchH
Q psy6490         325 AQPKE  329 (398)
Q Consensus       325 a~~k~  329 (398)
                      +..+.
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            88764

>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=99.76  E-value=9.9e-19  Score=132.37  Aligned_cols=84  Identities=26%  Similarity=0.452  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C------CCcccCCcc
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V------PIHTLDGKK  231 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~------~~~~~~g~~  231 (398)
                      .+.++|||+|||.++|+++|+++|++||.|.++.++.++.++.++|||||+|.+.++|.+|++ +      ++..++|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            367899999999999999999999999999999999999999999999999999999999997 3      366789999


Q ss_pred             cCCCCCCCCCC
Q psy6490         232 IDPKHATPKNR  242 (398)
Q Consensus       232 l~v~~~~~~~~  242 (398)
                      |.|.++.++..
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999876543

>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=99.76  E-value=1.3e-18  Score=133.03  Aligned_cols=83  Identities=22%  Similarity=0.494  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCC-CCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++|+++|+++|+.|| +++++++.++ .+++++|||||+|.+.++|++|+++++..|+|+.|+|.++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3568999999999999999999999999 7788877765 5788999999999999999999999999999999999998


Q ss_pred             CCCCC
Q psy6490         238 TPKNR  242 (398)
Q Consensus       238 ~~~~~  242 (398)
                      ..+..
T Consensus        92 ~~~~~   96 (104)
T d1wi8a_          92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76554

>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=99.76  E-value=8.5e-19  Score=128.61  Aligned_cols=77  Identities=13%  Similarity=0.286  Sum_probs=72.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++.+++ +|+++|||||+|.+.++|.+||++++..+.|+.|.|.+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            46899999999999999999999999999999998876 889999999999999999999999999999999998764

>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=99.75  E-value=3.6e-19  Score=137.91  Aligned_cols=88  Identities=17%  Similarity=0.299  Sum_probs=79.4

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEec
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKA  325 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a  325 (398)
                      .....+|||+|||+++|++||+++|+.||.|..+.++.+..+|.++|||||+|.+.++|++++++|+..|+||.|.|.++
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            34566899999999999999999999999998877777778999999999999999999999999999999999999999


Q ss_pred             CchHHHhh
Q psy6490         326 QPKEAVQA  333 (398)
Q Consensus       326 ~~k~~~~~  333 (398)
                      ..++....
T Consensus        95 ~~~~~~~~  102 (112)
T d1wela1          95 TKKGMLEK  102 (112)
T ss_dssp             CHHHHHHH
T ss_pred             ChHHHHHH
Confidence            88776543

>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=99.75  E-value=2.8e-18  Score=128.75  Aligned_cols=79  Identities=15%  Similarity=0.306  Sum_probs=69.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...++|||+|||.++|+++|+++|+.||.|..+.+..+   +.++|||||+|++.++|+.|+ .||++.|+|+.|+|+|+
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            44568999999999999999999999999999887654   456899999999988777666 69999999999999998


Q ss_pred             Cch
Q psy6490         326 QPK  328 (398)
Q Consensus       326 ~~k  328 (398)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>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=99.75  E-value=4e-18  Score=129.38  Aligned_cols=80  Identities=21%  Similarity=0.369  Sum_probs=73.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      .+.++|||+|||.++++++|+++|+.||.|.++++..+. ++.++|||||+|.+.++|.+|++ +|+..|.|+++.+.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            356899999999999999999999999999999998885 78899999999999999999997 8999999999998776


Q ss_pred             CC
Q psy6490         238 TP  239 (398)
Q Consensus       238 ~~  239 (398)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.75  E-value=7.9e-19  Score=136.73  Aligned_cols=102  Identities=11%  Similarity=0.281  Sum_probs=85.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++|+++|+++|++||.|++|++..+   +.++|||||+|.+.++|..|++ +++..|+|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            5689999999999999999999999999999999764   5579999999999999999997 89999999999998875


Q ss_pred             CCCCCccCccccceeecCCCCCCCHHHHHHHHhhcCC
Q psy6490         239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK  275 (398)
Q Consensus       239 ~~~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~  275 (398)
                      .....           ........+++++.++++||.
T Consensus        83 ~~~~~-----------~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          83 ANRAF-----------QKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHHHT-----------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CCchh-----------hhhHHHHHHHHHHHHHHHhCC
Confidence            32211           112223457888888888885

>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=99.75  E-value=8.7e-19  Score=131.93  Aligned_cols=84  Identities=18%  Similarity=0.382  Sum_probs=72.1

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCC-eeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHH-HHC--CceeCCEEEEEE
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGK-VEETVMLMDQ-QTKRHRGFGFVTFENEEVVDHIC-EIH--FHMIKNKKVECK  323 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~-i~~v~i~~~~-~~~~~kg~afV~F~~~eaa~a~~-~l~--~~~i~g~~i~v~  323 (398)
                      +++|||+|||.++|+++|+++|+.||. |+++++++|. .+++++|||||+|.+.++|..|+ .|+  +..++|+.|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            367999999999999999999999996 9999998885 46889999999999988777766 464  556789999999


Q ss_pred             ecCchHHHh
Q psy6490         324 KAQPKEAVQ  332 (398)
Q Consensus       324 ~a~~k~~~~  332 (398)
                      ||+++.+..
T Consensus        81 ~A~p~~~~~   89 (96)
T d2disa1          81 WAEPEIDVD   89 (96)
T ss_dssp             ESCSSCSTT
T ss_pred             EcCCCCCCC
Confidence            999876553

>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=99.75  E-value=1e-18  Score=128.76  Aligned_cols=78  Identities=18%  Similarity=0.232  Sum_probs=68.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ...+|||+|||++++++||+++|+.||.|....++.+..+++++|||||+|.+.++|++|+ +||+..|+||+|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3467999999999999999999999999987655566678999999999999988887665 69999999999999985

>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=99.74  E-value=3e-19  Score=132.13  Aligned_cols=78  Identities=31%  Similarity=0.631  Sum_probs=69.2

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecCc
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP  327 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~~  327 (398)
                      ..++|||+|||+++|+++|+++|++||.|.+|++.     ..++|||||+|++.++|++|++ +++.|+|+.|+|+|+.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            46789999999999999999999999999998764     3458999999999999988875 88999999999999987


Q ss_pred             hHHH
Q psy6490         328 KEAV  331 (398)
Q Consensus       328 k~~~  331 (398)
                      +...
T Consensus        78 k~~~   81 (88)
T d1wf0a_          78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.74  E-value=1.3e-18  Score=130.85  Aligned_cols=80  Identities=15%  Similarity=0.232  Sum_probs=70.1

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEe
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKK  324 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~  324 (398)
                      ....++|||+|||.++|+++|+++|+.||.|..++     .++.++|||||+|.+.++|++|+ .|||..|+|+.|+|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568899999999999999999999999887654     26788999999999988887766 6999999999999999


Q ss_pred             cCchHH
Q psy6490         325 AQPKEA  330 (398)
Q Consensus       325 a~~k~~  330 (398)
                      +.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            998754

>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=99.74  E-value=1.4e-18  Score=128.83  Aligned_cols=80  Identities=20%  Similarity=0.424  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ...+|||+|||.++|+++|+++|+.||.|.+++++.++  +.++|||||+|.+.++|++|++ +++..++|+.|.|.++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999986  3478999999999999999997 89999999999999987


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      ++.
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=6.9e-19  Score=127.62  Aligned_cols=75  Identities=16%  Similarity=0.333  Sum_probs=66.2

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCc-eeCCEEEEEEecCc
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFH-MIKNKKVECKKAQP  327 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~-~i~g~~i~v~~a~~  327 (398)
                      ++|||+|||.++|+++|+++|++||.|.++++.++      +|||||+|.+.++|+.|+ +|||. .|+|+.|+|+|+.+
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            46999999999999999999999999988777654      789999999988887666 69986 69999999999998


Q ss_pred             hHH
Q psy6490         328 KEA  330 (398)
Q Consensus       328 k~~  330 (398)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            754

>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=99.74  E-value=1.2e-19  Score=135.05  Aligned_cols=81  Identities=25%  Similarity=0.365  Sum_probs=74.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+++++.+ .+|+++|||||+|.+.++|++||++++..++|+.|.|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            336789999999999999999999999999998888655 4899999999999999999999999999999999999988


Q ss_pred             CC
Q psy6490         238 TP  239 (398)
Q Consensus       238 ~~  239 (398)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.74  E-value=2.1e-18  Score=126.77  Aligned_cols=76  Identities=25%  Similarity=0.539  Sum_probs=67.5

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++++++|+++|+.||.|.+|++.++      +|||||+|++.++|+.|+ .|||..|+|+.|+|+||.
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            3457999999999999999999999999999999866      689999999977776655 699999999999999998


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      .+.
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            653

>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=99.74  E-value=5.2e-18  Score=124.91  Aligned_cols=76  Identities=20%  Similarity=0.286  Sum_probs=67.0

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++|+++|+++|+.||.|..+.+.+      ++|||||+|.+.++|..|+ .|||..|+|+.|+|+|++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            457899999999999999999999999998777643      4889999999987776665 699999999999999998


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      +++
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.73  E-value=3.7e-18  Score=124.72  Aligned_cols=76  Identities=16%  Similarity=0.259  Sum_probs=66.8

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee-CCEEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI-KNKKVECK  323 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i-~g~~i~v~  323 (398)
                      ..++++|||+|||.++|+++|+++|+.||.|++|++++++     +|||||+|.+.++|.+|+ .|||..| +|+.|+|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            3457899999999999999999999999999999997653     789999999988777666 6899988 46899999


Q ss_pred             ecC
Q psy6490         324 KAQ  326 (398)
Q Consensus       324 ~a~  326 (398)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.73  E-value=3.3e-18  Score=130.14  Aligned_cols=84  Identities=14%  Similarity=0.232  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      ......+|||+|||+++|+++|+++|+.|| +.++.++.+. ++.++|||||+|.+.++|++|+++++..|+||.|+|.+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            334668999999999999999999999998 4577787775 68899999999999999999999999999999999998


Q ss_pred             CCCCCC
Q psy6490         237 ATPKNR  242 (398)
Q Consensus       237 ~~~~~~  242 (398)
                      +.....
T Consensus        89 s~~~~~   94 (102)
T d1weza_          89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             cCCCCC
Confidence            776554

>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=99.73  E-value=3.6e-18  Score=129.94  Aligned_cols=85  Identities=21%  Similarity=0.398  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEE--------EEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      ++...++|||+|||.++|+++|+++|+.||.|.        .+.+.+++.+|+++|||||+|.+.++|.+|++ +++..|
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            344778999999999999999999999999874        56777888899999999999999999999998 899999


Q ss_pred             CCcccCCCCCCCCC
Q psy6490         228 DGKKIDPKHATPKN  241 (398)
Q Consensus       228 ~g~~l~v~~~~~~~  241 (398)
                      +|+.|.|+++..+.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999987654

>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=99.73  E-value=2.7e-18  Score=127.79  Aligned_cols=82  Identities=17%  Similarity=0.352  Sum_probs=70.6

Q ss_pred             cccceeecCCCCCCCHHHHHH----HHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEE
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKA----YFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVEC  322 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~----~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v  322 (398)
                      ++++|||+|||.+++++||++    +|++||.|.+|++.+   ++.++|||||+|++.++|..|+ ++||..|+|+.|+|
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            467899999999999999865    689999999988754   4667999999999988777666 69999999999999


Q ss_pred             EecCchHHHh
Q psy6490         323 KKAQPKEAVQ  332 (398)
Q Consensus       323 ~~a~~k~~~~  332 (398)
                      .|++++.+..
T Consensus        79 ~~ak~~~~~~   88 (91)
T d1nu4a_          79 QYAKTDSDII   88 (91)
T ss_dssp             EECSSCCTHH
T ss_pred             EEeCCCchhh
Confidence            9999876553

>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=99.73  E-value=3.1e-18  Score=123.84  Aligned_cols=73  Identities=22%  Similarity=0.381  Sum_probs=64.8

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+||+  +|+++|+++|++||.|.+|++.++      +|||||+|++.++|..++ +|||..|+|+.|+|+|++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45789999985  999999999999999999998754      689999999987776555 799999999999999998


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.73  E-value=3.5e-18  Score=122.05  Aligned_cols=74  Identities=18%  Similarity=0.222  Sum_probs=68.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ++|||+|||.++++++|+++|+.||.|.++++.+++..  .++||||+|.+.++|.+|+++++..|+|+.|.|+..
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--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999998643  467999999999999999999999999999988654

>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=99.72  E-value=3.1e-18  Score=128.98  Aligned_cols=75  Identities=24%  Similarity=0.440  Sum_probs=65.6

Q ss_pred             CccccceeecCCC-CCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEE
Q psy6490         246 GNRTKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECK  323 (398)
Q Consensus       246 ~~~~~~l~V~nLp-~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~  323 (398)
                      ....++|||+||+ ..+++++|+++|++||.|++|+|        +||||||+|++.++|++|+ +|||+.|+|+.|+|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445679999996 67889999999999999999988        3789999999988887765 699999999999999


Q ss_pred             ecCch
Q psy6490         324 KAQPK  328 (398)
Q Consensus       324 ~a~~k  328 (398)
                      |+.++
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            99764

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=3.8e-18  Score=126.27  Aligned_cols=75  Identities=21%  Similarity=0.353  Sum_probs=66.1

Q ss_pred             ccceeecCCCCCCCHHHH---HHHHhhcCCeeEEEEeecCCCCCc---ceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         249 TKKIFVGGVSQDTSAEEV---KAYFSQFGKVEETVMLMDQQTKRH---RGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L---~~~F~~~G~i~~v~i~~~~~~~~~---kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      .++|||+|||++++++||   +++|++||.|++|.|++|+.++.+   +|||||+|++.++|+.|+ +|||..|+||.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            457999999999999999   678999999999999999776654   499999999977776655 7999999999999


Q ss_pred             EE
Q psy6490         322 CK  323 (398)
Q Consensus       322 v~  323 (398)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.1e-18  Score=124.06  Aligned_cols=70  Identities=17%  Similarity=0.497  Sum_probs=65.4

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEE
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVE  321 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~  321 (398)
                      |||+|||.++|+++|+++|++||.|.++++.+++.++.++|||||+|.+.++|++|+ .|||..|+|+.|+
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            799999999999999999999999999999999999999999999999988887666 6999999999764

>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=99.71  E-value=3.1e-18  Score=121.62  Aligned_cols=70  Identities=20%  Similarity=0.473  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       164 l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      |||+|||.++|+++|+++|+.||.|.++++.+++.++.++|||||+|.+.++|++|++ +++..++|+.|+
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            7999999999999999999999999999999999999999999999999999999997 899999998874

>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=99.71  E-value=1.7e-18  Score=132.02  Aligned_cols=83  Identities=27%  Similarity=0.286  Sum_probs=78.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ++++|||+|||.++++++|+++|+.||.|.++.+..+..+|+++|||||+|.+.++|.+|++ +++..|+|+.|.|.++.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            67899999999999999999999999999999999888889999999999999999999997 89999999999999998


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      .+..
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            7554

>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=99.71  E-value=7e-18  Score=130.21  Aligned_cols=76  Identities=11%  Similarity=0.291  Sum_probs=67.0

Q ss_pred             ccceeecCCC-CCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         249 TKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       249 ~~~l~V~nLp-~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      +++|||+||+ ..+|+++|+++|+.||.|++|+|++++     +|||||+|++.++|.+|+ .|||..|.|+.|+|+|++
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            4689999995 569999999999999999999998874     789999999987776665 699999999999999987


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      .+.
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.71  E-value=1.1e-17  Score=123.54  Aligned_cols=75  Identities=19%  Similarity=0.301  Sum_probs=63.1

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      .+++|||+|||.+++++||+++|++|| ++.+.+      ++++|||||+|++.++|++|+ +||+..|+|+.|+|+|++
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-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 333333      345899999999987776665 799999999999999997


Q ss_pred             chH
Q psy6490         327 PKE  329 (398)
Q Consensus       327 ~k~  329 (398)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.71  E-value=1.9e-17  Score=122.34  Aligned_cols=78  Identities=21%  Similarity=0.317  Sum_probs=69.3

Q ss_pred             CccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH---HCCceeCCEEEEE
Q psy6490         246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE---IHFHMIKNKKVEC  322 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~---l~~~~i~g~~i~v  322 (398)
                      ..++++|||+|||.++++++|+++|++||.|.++++.++      +|||||+|++.++|+++++   +++..++|+.|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            457889999999999999999999999999999998765      6799999999888877654   5788999999999


Q ss_pred             EecCchH
Q psy6490         323 KKAQPKE  329 (398)
Q Consensus       323 ~~a~~k~  329 (398)
                      .|++.++
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9998664

>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=99.71  E-value=8.7e-18  Score=126.09  Aligned_cols=76  Identities=17%  Similarity=0.470  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|+.||.|.+|++.++      ||||||+|.+.++|++|++ +++..++|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4579999999999999999999999999999999976      7899999999999999997 89999999999999986


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      .+.
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.71  E-value=6.5e-18  Score=130.88  Aligned_cols=75  Identities=15%  Similarity=0.171  Sum_probs=66.3

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~  326 (398)
                      ..++|||+|||.++++++|+++|+.||.|.+|.|.      .++|||||+|.+.++|.+|+ +|||..|.|+.|.|+|+.
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 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            45789999999999999999999999999998874      34799999999987776655 799999999999999986


Q ss_pred             ch
Q psy6490         327 PK  328 (398)
Q Consensus       327 ~k  328 (398)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.71  E-value=1.6e-17  Score=121.26  Aligned_cols=76  Identities=16%  Similarity=0.272  Sum_probs=68.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc-CCcccCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL-DGKKIDPK  235 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~-~g~~l~v~  235 (398)
                      ++++++|||+|||.++|+++|+++|+.||.|.+|+++++     .+|||||+|.+.++|.+|++ +++..+ +|+.|.|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            346789999999999999999999999999999999876     37899999999999999998 788877 56889988


Q ss_pred             CCC
Q psy6490         236 HAT  238 (398)
Q Consensus       236 ~~~  238 (398)
                      |++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            875

>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=99.70  E-value=1.8e-17  Score=122.46  Aligned_cols=77  Identities=16%  Similarity=0.316  Sum_probs=66.2

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee-CCEEEEEEe
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI-KNKKVECKK  324 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i-~g~~i~v~~  324 (398)
                      .++++|||+|||.++|+++|+++|++||.|.++++..+    +++|||||+|++.++|.+++ +|||..| +|+.|+|+|
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            35678999999999999999999999999988876544    34789999999977776655 7999988 589999999


Q ss_pred             cCc
Q psy6490         325 AQP  327 (398)
Q Consensus       325 a~~  327 (398)
                      +++
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=99.70  E-value=3.3e-17  Score=122.82  Aligned_cols=78  Identities=18%  Similarity=0.410  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++|+++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|++||+ +++..|+|++|.|+++.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            5678999999999999999999999999999987654   4468999999999999999997 89999999999999987


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.70  E-value=2.3e-18  Score=126.97  Aligned_cols=75  Identities=19%  Similarity=0.233  Sum_probs=66.0

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      ++|||+|||+++++++|+++|++||.|.++.|.+|       |||||+|.+.++|++|+ +|||..|+|+.|+|.+++.+
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            36999999999999999999999999999998644       79999999988877766 79999999999999988765


Q ss_pred             HHH
Q psy6490         329 EAV  331 (398)
Q Consensus       329 ~~~  331 (398)
                      ...
T Consensus        74 ~~~   76 (87)
T d3begb1          74 VDG   76 (87)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            443

>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=99.70  E-value=5.8e-18  Score=125.06  Aligned_cols=77  Identities=31%  Similarity=0.550  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~  239 (398)
                      .+++|||+|||.++|+++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|+. ++..|+|+.|.|+++.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            5789999999999999999999999999999987544     68999999999999999997 67889999999999876


Q ss_pred             CCC
Q psy6490         240 KNR  242 (398)
Q Consensus       240 ~~~  242 (398)
                      +..
T Consensus        78 k~~   80 (88)
T d1wf0a_          78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.70  E-value=7.3e-18  Score=130.44  Aligned_cols=81  Identities=15%  Similarity=0.297  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA  237 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~  237 (398)
                      ....++|||+|||+++|+++|+++|+.||.+.++.++.+..+|.++|||||+|.+.++|++|+++++..|+||.|.|..+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            34677999999999999999999999999988776777777999999999999999999999999999999999988665


Q ss_pred             C
Q psy6490         238 T  238 (398)
Q Consensus       238 ~  238 (398)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.70  E-value=1.8e-17  Score=124.57  Aligned_cols=83  Identities=22%  Similarity=0.379  Sum_probs=72.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcCCC-EEEEEEeeCC-CCCCcccEEEEEEcChHhHHHHHh-CC--CcccCCcccCCC
Q psy6490         161 SAKLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDP-ITQRSRGFGFITFAEPETVEKVLK-VP--IHTLDGKKIDPK  235 (398)
Q Consensus       161 ~~~l~v~nLp~~~t~~~L~~~f~~~G~-i~~~~~~~~~-~~~~~~g~afV~f~~~e~a~~al~-~~--~~~~~g~~l~v~  235 (398)
                      +++|||+|||.++|+++|+++|+.||+ |.+++++++. .+++++|||||+|.+.++|.+|++ ++  +..++|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999995 9999999885 468899999999999999999998 53  445689999999


Q ss_pred             CCCCCCCC
Q psy6490         236 HATPKNRP  243 (398)
Q Consensus       236 ~~~~~~~~  243 (398)
                      |+.++...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99876554

>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=99.70  E-value=1.8e-17  Score=124.73  Aligned_cols=75  Identities=15%  Similarity=0.415  Sum_probs=67.6

Q ss_pred             CCCcEEEEcCCC-CCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         159 PTSAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       159 ~~~~~l~v~nLp-~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ...++|||+||+ ..+++++|+++|++||.|++|++        ++|||||+|.+.++|++||+ +++..|.|++|.|.+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356789999996 57889999999999999999998        47899999999999999998 899999999999999


Q ss_pred             CCCCC
Q psy6490         237 ATPKN  241 (398)
Q Consensus       237 ~~~~~  241 (398)
                      +....
T Consensus        85 a~~~~   89 (98)
T d1wf2a_          85 AAEPK   89 (98)
T ss_dssp             TTSCC
T ss_pred             CCCCC
Confidence            87543

>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=99.69  E-value=4.1e-17  Score=122.75  Aligned_cols=76  Identities=18%  Similarity=0.447  Sum_probs=66.8

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCC--EEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKN--KKVECK  323 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g--~~i~v~  323 (398)
                      .++++|||+|||.++++++|+++|++||.|+++++.++      ++||||+|.+.++|+.++ .||+..|+|  ++|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            45689999999999999999999999999999998765      689999999987776655 799999986  589999


Q ss_pred             ecCch
Q psy6490         324 KAQPK  328 (398)
Q Consensus       324 ~a~~k  328 (398)
                      |++++
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            99754

>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=99.69  E-value=1.9e-17  Score=121.56  Aligned_cols=76  Identities=30%  Similarity=0.531  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|+.||.|.+|++.++      +|||||+|.+.++|++|++ +++..++|+.|.|+++.
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            4568999999999999999999999999999999865      7899999999999999998 89999999999999987


Q ss_pred             CCC
Q psy6490         239 PKN  241 (398)
Q Consensus       239 ~~~  241 (398)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            654

>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=99.69  E-value=1.4e-17  Score=125.13  Aligned_cols=81  Identities=21%  Similarity=0.293  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPK  235 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~  235 (398)
                      ...+.++|||+|||.++|+++|+++|+.||.|..++.     ++.++|||||+|.+.++|++|++ +++..|+|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3446799999999999999999999999998876543     67789999999999999999997 99999999999999


Q ss_pred             CCCCCCC
Q psy6490         236 HATPKNR  242 (398)
Q Consensus       236 ~~~~~~~  242 (398)
                      ++.++..
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9887654

>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=99.69  E-value=5.2e-17  Score=115.85  Aligned_cols=70  Identities=19%  Similarity=0.391  Sum_probs=60.7

Q ss_pred             eeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEecCch
Q psy6490         252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKAQPK  328 (398)
Q Consensus       252 l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a~~k  328 (398)
                      |||+|||.++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|+ +|||..++|+.|+|+|+..+
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-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444443      456899999999987776665 79999999999999999765

>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=99.68  E-value=8.4e-18  Score=128.24  Aligned_cols=80  Identities=8%  Similarity=0.138  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~  238 (398)
                      ....+|||+|||+++|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|++||++++..|+|+.|.|.++.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            35678999999999999999999999999887666666669999999999999999999999999999999999987654

>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=99.68  E-value=4.3e-17  Score=120.43  Aligned_cols=76  Identities=20%  Similarity=0.276  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc-CCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL-DGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~-~g~~l~v~~~  237 (398)
                      ++++|||+|||.++++++|+++|++||.|.++.+..++    ++|||||+|.+.++|.+|+. +++..+ +|+.|+|.++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~----~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec----ccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            67899999999999999999999999999888776543    58899999999999999997 888877 6899999987


Q ss_pred             CC
Q psy6490         238 TP  239 (398)
Q Consensus       238 ~~  239 (398)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.68  E-value=4.6e-17  Score=125.55  Aligned_cols=75  Identities=21%  Similarity=0.356  Sum_probs=69.1

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         161 SAKLFVGGLSW-QTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       161 ~~~l~v~nLp~-~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      +++|||+||++ .+|+++|+++|+.||.|++|+|++++     +|||||+|.+.++|.+|++ +++..|.|+.|.|.++.
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            57999999954 69999999999999999999999884     8999999999999999998 89999999999999986


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.68  E-value=8.6e-18  Score=124.30  Aligned_cols=75  Identities=25%  Similarity=0.467  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCCCHHHH---HHHHhcCCCEEEEEEeeCCCCCCc---ccEEEEEEcChHhHHHHHh-CCCcccCCccc
Q psy6490         160 TSAKLFVGGLSWQTSSEKL---REYFGMFGAVTDVLIMKDPITQRS---RGFGFITFAEPETVEKVLK-VPIHTLDGKKI  232 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L---~~~f~~~G~i~~~~~~~~~~~~~~---~g~afV~f~~~e~a~~al~-~~~~~~~g~~l  232 (398)
                      ..++|||+|||+++++++|   +++|++||.|.+|.+++++.++.+   +|||||+|.+.++|.+|++ +|+..++|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            5678999999999999999   678999999999999999877654   4899999999999999997 89999999998


Q ss_pred             CC
Q psy6490         233 DP  234 (398)
Q Consensus       233 ~v  234 (398)
                      ++
T Consensus        87 kv   88 (89)
T d2cpia1          87 KA   88 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=99.68  E-value=4.2e-17  Score=125.34  Aligned_cols=79  Identities=11%  Similarity=0.172  Sum_probs=68.6

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCcee--CCEEEEEE
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMI--KNKKVECK  323 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i--~g~~i~v~  323 (398)
                      ....+|||+||++++|+++|+++|++||.|++|+|++++    ++|||||+|++.++|+.|+ .|||..|  +|++|+|.
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            356789999999999999999999999999999998774    4899999999977776655 7999988  58899999


Q ss_pred             ecCchH
Q psy6490         324 KAQPKE  329 (398)
Q Consensus       324 ~a~~k~  329 (398)
                      |++.+.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            987754

>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=99.67  E-value=1.5e-17  Score=122.36  Aligned_cols=77  Identities=9%  Similarity=0.197  Sum_probs=68.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~  236 (398)
                      ..++|||+|||.++++++|+++|+.||.+.+..++.+..+++++|||||+|.+.++|++|++ +++..++||+|+|+.
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            55789999999999999999999999998775444445589999999999999999999997 899999999998764

>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=99.67  E-value=3.5e-17  Score=123.42  Aligned_cols=78  Identities=12%  Similarity=0.187  Sum_probs=68.3

Q ss_pred             CccccceeecCCCCC-CCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH---HHCCceeCCEEEE
Q psy6490         246 GNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC---EIHFHMIKNKKVE  321 (398)
Q Consensus       246 ~~~~~~l~V~nLp~~-~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~---~l~~~~i~g~~i~  321 (398)
                      ...+++|||+|||.+ +|+++|+++|++||.|.+++++++      +|||||+|++.++|..|+   ++++..|+|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345678999999985 899999999999999999999765      689999999988887765   4799999999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |.|++.+.
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997653

>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=99.67  E-value=1e-16  Score=122.24  Aligned_cols=79  Identities=14%  Similarity=0.173  Sum_probs=69.0

Q ss_pred             cCccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-H--CCceeCCEEEE
Q psy6490         245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I--HFHMIKNKKVE  321 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~-l--~~~~i~g~~i~  321 (398)
                      ....+++|||+|||.++||+||+++|++||.|+++++.++      ||||||+|++.++|++|++ +  ++..++|+.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3456789999999999999999999999999999998755      7899999999888877664 4  67789999999


Q ss_pred             EEecCchH
Q psy6490         322 CKKAQPKE  329 (398)
Q Consensus       322 v~~a~~k~  329 (398)
                      |.|++.+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997654

>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=99.66  E-value=2.3e-16  Score=120.18  Aligned_cols=80  Identities=18%  Similarity=0.216  Sum_probs=70.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-C--CCcccCCcccC
Q psy6490         157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V--PIHTLDGKKID  233 (398)
Q Consensus       157 ~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~--~~~~~~g~~l~  233 (398)
                      ...++++|||+|||.++||++|+++|+.||.|.++++.++      ||||||+|.+.++|++|++ +  +...++|++|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3447899999999999999999999999999999999764      7899999999999999997 3  56678999999


Q ss_pred             CCCCCCCCC
Q psy6490         234 PKHATPKNR  242 (398)
Q Consensus       234 v~~~~~~~~  242 (398)
                      |.++..+..
T Consensus        85 v~~s~~~~~   93 (104)
T d1wexa_          85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEcCCCcc
Confidence            999876543

>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=99.66  E-value=9.7e-17  Score=117.94  Aligned_cols=77  Identities=25%  Similarity=0.370  Sum_probs=69.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||.++++++|+++|+.||.|..+++.+      ++|||||+|.+.++|.+|++ +++..|+|+.|.|.++.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            458999999999999999999999999988877754      48899999999999999998 89999999999999988


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      +..+
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6654

>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=99.66  E-value=1e-16  Score=120.54  Aligned_cols=74  Identities=18%  Similarity=0.254  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+|||+++++++|+++|++||+|+++++.+       +|||||+|.+.++|++||+ +|+..|+|+.|.|.+..
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            567899999999999999999999999999999864       5899999999999999997 89999999999998875


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      .+
T Consensus        87 ~~   88 (98)
T d1wg4a_          87 VY   88 (98)
T ss_dssp             EE
T ss_pred             cC
Confidence            43

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=2.8e-17  Score=127.22  Aligned_cols=75  Identities=17%  Similarity=0.267  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.++++++|+++|+.||+|.+|.|.+      ++|||||+|.+.++|.+|++ +++..|.|+.|.|.++.
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            568999999999999999999999999999998843      48999999999999999997 89999999999998875


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.66  E-value=4.5e-17  Score=122.51  Aligned_cols=77  Identities=14%  Similarity=0.202  Sum_probs=68.0

Q ss_pred             ccccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       247 ~~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ....+|||+|||++++++||+++|++||.|+++.|.+       +|||||+|.+.++|++|+ +|||..|+|+.|+|.++
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            3456799999999999999999999999999998853       579999999988887776 69999999999999998


Q ss_pred             CchHH
Q psy6490         326 QPKEA  330 (398)
Q Consensus       326 ~~k~~  330 (398)
                      +.+.+
T Consensus        86 ~~~~~   90 (98)
T d1wg4a_          86 RVYPE   90 (98)
T ss_dssp             EEECC
T ss_pred             ecCCC
Confidence            76653

>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=99.66  E-value=1.6e-17  Score=120.32  Aligned_cols=75  Identities=20%  Similarity=0.389  Sum_probs=67.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCc-ccCCcccCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIH-TLDGKKIDPKHATP  239 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~-~~~g~~l~v~~~~~  239 (398)
                      ++|||+|||.++|+++|+++|++||.|.++++.++      +|||||+|.+.++|++|++ +++. .++|+.|.|.++.+
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            47999999999999999999999999888777664      8999999999999999997 8875 59999999999987


Q ss_pred             CCC
Q psy6490         240 KNR  242 (398)
Q Consensus       240 ~~~  242 (398)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>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=99.66  E-value=8.4e-19  Score=130.41  Aligned_cols=76  Identities=11%  Similarity=0.333  Sum_probs=67.2

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEe-----ecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEe
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML-----MDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK  324 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~-----~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~  324 (398)
                      ++|||+|||+++||++|+++|+.||.|..+.+.     .+..+++++|||||+|.+.|+|++|++|||..++|+.|+|++
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            579999999999999999999999988766553     455678899999999999888888889999999999999975


Q ss_pred             c
Q psy6490         325 A  325 (398)
Q Consensus       325 a  325 (398)
                      .
T Consensus        82 ~   82 (90)
T d1u2fa_          82 P   82 (90)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.65  E-value=9.7e-17  Score=118.41  Aligned_cols=78  Identities=10%  Similarity=0.139  Sum_probs=67.9

Q ss_pred             cCccccceeecCCCCC-CCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH---HCCceeCCEEE
Q psy6490         245 IGNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE---IHFHMIKNKKV  320 (398)
Q Consensus       245 ~~~~~~~l~V~nLp~~-~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~---l~~~~i~g~~i  320 (398)
                      ..+.+++|||+|||.. +|++||+++|++||.|.+|+++++      +++|||+|++.++|..|++   +++..++|+.|
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 889999999999999999999766      5699999999888877653   58899999999


Q ss_pred             EEEecCch
Q psy6490         321 ECKKAQPK  328 (398)
Q Consensus       321 ~v~~a~~k  328 (398)
                      +|.|++..
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99999754

>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=99.65  E-value=2.3e-16  Score=118.54  Aligned_cols=76  Identities=22%  Similarity=0.400  Sum_probs=68.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCc--ccCCC
Q psy6490         159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGK--KIDPK  235 (398)
Q Consensus       159 ~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~--~l~v~  235 (398)
                      .++++|||+|||.++++++|+++|++||.|.++++.++      ++||||+|.+.++|++|++ +++..|+|+  +|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            36799999999999999999999999999999999765      7899999999999999997 789988774  68888


Q ss_pred             CCCCC
Q psy6490         236 HATPK  240 (398)
Q Consensus       236 ~~~~~  240 (398)
                      +++..
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            87654

>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=99.65  E-value=7.4e-17  Score=116.43  Aligned_cols=73  Identities=19%  Similarity=0.355  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      ..++|||+||+  +|+++|+++|++||.|.++++.++      +|||||+|.+.++|.+|++ +++..++|++|.|.++.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            56899999985  999999999999999999999764      7899999999999999997 89999999999999986


Q ss_pred             CC
Q psy6490         239 PK  240 (398)
Q Consensus       239 ~~  240 (398)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.65  E-value=5.5e-17  Score=119.45  Aligned_cols=71  Identities=15%  Similarity=0.232  Sum_probs=65.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATP  239 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~  239 (398)
                      ++|||+|||.++++++|+++|++||.|.++++.+       +|||||+|.+.++|++||+ +++..|+|+.|.|.+...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            3699999999999999999999999999999865       3799999999999999997 999999999999987654

>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=99.65  E-value=1.4e-16  Score=117.56  Aligned_cols=78  Identities=19%  Similarity=0.253  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh---CCCcccCCcccCC
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK---VPIHTLDGKKIDP  234 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~---~~~~~~~g~~l~v  234 (398)
                      ..++++|||+|||.++++++|+++|+.||.|.++++.++      +|||||+|.+.++|++|++   .++..++|+.|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            448899999999999999999999999999999999865      6899999999999999987   3677899999999


Q ss_pred             CCCCCCC
Q psy6490         235 KHATPKN  241 (398)
Q Consensus       235 ~~~~~~~  241 (398)
                      .+++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9987554

>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=99.65  E-value=1e-16  Score=123.15  Aligned_cols=78  Identities=12%  Similarity=0.257  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc--CCcccCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL--DGKKIDPKH  236 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~--~g~~l~v~~  236 (398)
                      +..+|||+||++++|+++|+++|++||.|.+|++.+++    ++|||||+|.+.++|++|++ +++..|  .+++|.+.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            67899999999999999999999999999999999875    58999999999999999998 788877  577888877


Q ss_pred             CCCCC
Q psy6490         237 ATPKN  241 (398)
Q Consensus       237 ~~~~~  241 (398)
                      +..+.
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            76544

>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=99.64  E-value=1.1e-17  Score=124.18  Aligned_cols=78  Identities=12%  Similarity=0.315  Sum_probs=68.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEe-----eCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM-----KDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH  236 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~-----~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~  236 (398)
                      ++|||+|||.++|+++|+++|+.||.+.++.+.     .+..+++++|||||+|.+.++|++|+++++..+.|+.|.|++
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            789999999999999999999999987766553     344577899999999999999999999999999999999986


Q ss_pred             CCC
Q psy6490         237 ATP  239 (398)
Q Consensus       237 ~~~  239 (398)
                      .+.
T Consensus        82 ~k~   84 (90)
T d1u2fa_          82 PHD   84 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.64  E-value=5.3e-17  Score=120.63  Aligned_cols=79  Identities=19%  Similarity=0.429  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHH----HHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDP  234 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~----~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v  234 (398)
                      ++++|||+|||.++++++|++    +|++||.|.+|++.+   +++++|||||+|.+.++|.+|++ +++..++|+.|.|
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            568999999999999999864    689999999988754   46689999999999999999997 8999999999999


Q ss_pred             CCCCCCC
Q psy6490         235 KHATPKN  241 (398)
Q Consensus       235 ~~~~~~~  241 (398)
                      .++..+.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9987654

>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=99.62  E-value=1.6e-16  Score=117.05  Aligned_cols=76  Identities=12%  Similarity=0.265  Sum_probs=65.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .+++|||+|||.+++++||+++|++|| +..+.+      +.++|||||+|.+.++|++|++ +++..++|++|.|+++.
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-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            467999999999999999999999999 333333      2368999999999999999997 89999999999999986


Q ss_pred             CCCC
Q psy6490         239 PKNR  242 (398)
Q Consensus       239 ~~~~  242 (398)
                      .+..
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.62  E-value=3.1e-16  Score=132.53  Aligned_cols=130  Identities=25%  Similarity=0.392  Sum_probs=99.4

Q ss_pred             CCCCCCCCCCChhhHhhhhCCCccccccceeeeecCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHhcCCC
Q psy6490         108 DSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA  187 (398)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~  187 (398)
                      ..++++..+.+...+..+...................   ..............++|||+|||.++|+++|+++|+.||.
T Consensus        47 ~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~  123 (183)
T d1u1qa_          47 SRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV---SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK  123 (183)
T ss_dssp             EEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC---CTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSC
T ss_pred             ccCceecccCCHHHHHHHHHhcCCcccccchhhhhhh---hcccccccccccccceeEEccCCCcCCHHHHhhhhccCCc
Confidence            3457778888888888777655433222211111111   1111112233447789999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcccCCCCCCCC
Q psy6490         188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       188 i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~~~  240 (398)
                      |..+.++.+..+|.++|||||+|.+.++|.+|+++++..++|+.|.|+++.++
T Consensus       124 v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         124 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEECCCH
T ss_pred             eeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEecCCc
Confidence            99999999999999999999999999999999999899999999999887653

>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=99.61  E-value=1e-16  Score=121.73  Aligned_cols=75  Identities=13%  Similarity=0.189  Sum_probs=68.0

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCceeCCEEEEEEec
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFHMIKNKKVECKKA  325 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~~i~g~~i~v~~a  325 (398)
                      ..++|+++..+++||+|+++|++||.|++|+|.++ .+++++|||||+|++.++|.+|+ +|||+.++||.|+|+|+
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            46899999999999999999999999999999877 68999999999999977776555 79999999999999985

>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=99.60  E-value=3.8e-16  Score=117.64  Aligned_cols=78  Identities=10%  Similarity=0.196  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh---CCCcccCCcccC
Q psy6490         158 DPTSAKLFVGGLSWQ-TSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK---VPIHTLDGKKID  233 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~-~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~---~~~~~~~g~~l~  233 (398)
                      ...+++|||+|||.+ +|+++|+++|+.||.|.++++.++      +|||||+|.+.++|.+|++   +++..++|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            346789999999985 899999999999999999999865      7899999999999999986   678889999999


Q ss_pred             CCCCCCCC
Q psy6490         234 PKHATPKN  241 (398)
Q Consensus       234 v~~~~~~~  241 (398)
                      |.++..+.
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99886543

>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=99.60  E-value=6e-16  Score=110.23  Aligned_cols=70  Identities=11%  Similarity=0.320  Sum_probs=62.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCCCC
Q psy6490         164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPK  240 (398)
Q Consensus       164 l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~~~  240 (398)
                      |||+|||.++++++|+++|++|| +..+++.      +++|||||+|.+.++|++|++ +|+..++|++|.|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555543      368999999999999999997 9999999999999988654

>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=99.58  E-value=7.1e-16  Score=116.99  Aligned_cols=77  Identities=14%  Similarity=0.095  Sum_probs=64.6

Q ss_pred             cccceeecCCCCCC-C----HHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHH-HHHHHHCCceeCCEEEE
Q psy6490         248 RTKKIFVGGVSQDT-S----AEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV-DHICEIHFHMIKNKKVE  321 (398)
Q Consensus       248 ~~~~l~V~nLp~~~-t----ee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa-~a~~~l~~~~i~g~~i~  321 (398)
                      ..++|||+||+.++ +    +++|+++|+.||.|.++.++++      +|||||+|++.++| +|+.+|||..|+|+.|+
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 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            46789999999876 3    3579999999999999998754      78999999996655 55557999999999999


Q ss_pred             EEecCchHH
Q psy6490         322 CKKAQPKEA  330 (398)
Q Consensus       322 v~~a~~k~~  330 (398)
                      |.|++++..
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999976644

>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=99.57  E-value=1.1e-15  Score=112.58  Aligned_cols=78  Identities=15%  Similarity=0.187  Sum_probs=69.1

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh---CCCcccCCcccC
Q psy6490         158 DPTSAKLFVGGLSWQ-TSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK---VPIHTLDGKKID  233 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~-~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~---~~~~~~~g~~l~  233 (398)
                      .+.+++|||+|||.. +|++||+++|+.||.|.++++.++      +++|||+|.+.++|..|++   .++..++|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            347899999999986 889999999999999999999876      6799999999999999997   367789999999


Q ss_pred             CCCCCCCC
Q psy6490         234 PKHATPKN  241 (398)
Q Consensus       234 v~~~~~~~  241 (398)
                      |.++....
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99986543

>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=99.52  E-value=9.6e-15  Score=104.99  Aligned_cols=76  Identities=13%  Similarity=0.164  Sum_probs=64.9

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEE-EEEEecC
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKK-VECKKAQ  326 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~-i~v~~a~  326 (398)
                      ..+.|+|.|+|++.+++.| ++|++||.|.++++.+      .+|||||+|++.++|++|+++||..|+|+. |.|+.+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            3567999999999986555 5899999999998743      378999999999999888899999999974 6799998


Q ss_pred             chHH
Q psy6490         327 PKEA  330 (398)
Q Consensus       327 ~k~~  330 (398)
                      .|..
T Consensus        76 ~k~~   79 (81)
T d1wwha1          76 DKNV   79 (81)
T ss_dssp             CHHH
T ss_pred             Chhh
Confidence            8763

>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=99.51  E-value=6.6e-15  Score=113.59  Aligned_cols=77  Identities=14%  Similarity=0.196  Sum_probs=64.4

Q ss_pred             ccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCC-HHHH-HHHHHHCCceeCCEEEEEEecC
Q psy6490         249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV-DHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       249 ~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~-~eaa-~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      ...+||+||++++|+++|+++|++||.|.+|.|+++      +|||||+|.+ .++| .++.++++..+.++.+.|.|+.
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            445699999999999999999999999999999865      7899999998 4555 6677899999888887777766


Q ss_pred             chHHH
Q psy6490         327 PKEAV  331 (398)
Q Consensus       327 ~k~~~  331 (398)
                      .+.+.
T Consensus        85 ~~~~~   89 (113)
T d1owxa_          85 LEGEV   89 (113)
T ss_dssp             CCHHH
T ss_pred             ccchh
Confidence            55443

>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=99.51  E-value=5.6e-15  Score=111.95  Aligned_cols=77  Identities=18%  Similarity=0.116  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCC-CH----HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccC
Q psy6490         160 TSAKLFVGGLSWQT-SS----EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKID  233 (398)
Q Consensus       160 ~~~~l~v~nLp~~~-t~----~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~  233 (398)
                      .+++|||+||+.++ ++    ++|+++|+.||.|+++++++      +++||||+|.+.++|.+|++ +++..|+|+.|.
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            56899999999986 33    56999999999999999985      47899999999999999998 999999999999


Q ss_pred             CCCCCCCCC
Q psy6490         234 PKHATPKNR  242 (398)
Q Consensus       234 v~~~~~~~~  242 (398)
                      |.++.....
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999876543

>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=99.47  E-value=1.6e-15  Score=115.05  Aligned_cols=75  Identities=15%  Similarity=0.182  Sum_probs=69.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      +.++|+++..+++|++|+++|++||+|++|+|.++. +++++|||||+|.+.++|.+|++ +++..++||+|.|+++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            568899999999999999999999999999998774 89999999999999999999998 8999999999988764

>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=99.46  E-value=5e-14  Score=106.05  Aligned_cols=63  Identities=14%  Similarity=0.309  Sum_probs=53.4

Q ss_pred             ccccceeec--CCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH-HHHCCcee
Q psy6490         247 NRTKKIFVG--GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMI  315 (398)
Q Consensus       247 ~~~~~l~V~--nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~-~~l~~~~i  315 (398)
                      .++++|||.  ||+.++|+++|+++|++||.|++|++.++      +|||||+|.+.++|.+| .+|||+.|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456678885  59999999999999999999999988765      67999999997766555 57999987

>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=99.45  E-value=5.6e-14  Score=105.40  Aligned_cols=80  Identities=13%  Similarity=0.255  Sum_probs=65.9

Q ss_pred             CccccceeecCC--CCCC---------CHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH-HHCCc
Q psy6490         246 GNRTKKIFVGGV--SQDT---------SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIHFH  313 (398)
Q Consensus       246 ~~~~~~l~V~nL--p~~~---------tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~-~l~~~  313 (398)
                      ...+++|+|+||  +.++         .++||++.|++||.|..|.+..+    ..+|||||+|++.++|..|+ .|||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            456789999999  5433         23789999999999999987654    45799999999988776655 79999


Q ss_pred             eeCCEEEEEEecCchH
Q psy6490         314 MIKNKKVECKKAQPKE  329 (398)
Q Consensus       314 ~i~g~~i~v~~a~~k~  329 (398)
                      .|+||.|+|.++.++.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999987664

>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=99.41  E-value=8.8e-14  Score=99.85  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=62.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCcc-cCCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKK-IDPKHAT  238 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~~-l~v~~~~  238 (398)
                      +.+.|+|+++|++++++.| ++|++||+|.++++.+      ++|||||+|.++++|++||++|+..++|+. |.|+...
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            4678999999999987655 5799999999998754      478999999999999999999999999985 5566654


Q ss_pred             C
Q psy6490         239 P  239 (398)
Q Consensus       239 ~  239 (398)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.41  E-value=1.3e-13  Score=103.68  Aligned_cols=62  Identities=18%  Similarity=0.306  Sum_probs=55.2

Q ss_pred             CCcEEEEc--CCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         160 TSAKLFVG--GLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       160 ~~~~l~v~--nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      ++++|||+  ||+.++|+++|+++|++||.|.+|++.++      ++||||+|.+.++|.+|++ +++..+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            66888885  59999999999999999999999988765      6799999999999999997 666654

>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=99.38  E-value=3.4e-13  Score=103.72  Aligned_cols=73  Identities=21%  Similarity=0.186  Sum_probs=61.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcCh-HhHHHHHh-CCCcccCCcccCCCCC
Q psy6490         160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKVLK-VPIHTLDGKKIDPKHA  237 (398)
Q Consensus       160 ~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~-e~a~~al~-~~~~~~~g~~l~v~~~  237 (398)
                      ....+|||||+.++|+++|+++|++||+|.+|+|+++      +|||||.|.+. ++|..|+. +++..+.++.+.|.+.
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            4566799999999999999999999999999999865      78999999996 67877776 7777777777666554


Q ss_pred             C
Q psy6490         238 T  238 (398)
Q Consensus       238 ~  238 (398)
                      .
T Consensus        84 ~   84 (113)
T d1owxa_          84 V   84 (113)
T ss_dssp             E
T ss_pred             e
Confidence            3

>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=99.37  E-value=2.4e-13  Score=103.01  Aligned_cols=84  Identities=17%  Similarity=0.164  Sum_probs=67.4

Q ss_pred             ccccceeecCC--CCCCC--------HHHHHHHHhhcCCeeEEEEeecCCC--CCcceEEEEEeCCHHHHHH-HHHHCCc
Q psy6490         247 NRTKKIFVGGV--SQDTS--------AEEVKAYFSQFGKVEETVMLMDQQT--KRHRGFGFVTFENEEVVDH-ICEIHFH  313 (398)
Q Consensus       247 ~~~~~l~V~nL--p~~~t--------ee~L~~~F~~~G~i~~v~i~~~~~~--~~~kg~afV~F~~~eaa~a-~~~l~~~  313 (398)
                      .++++|+|+||  +.++.        .+||++.|++||.|++|.|.++..+  ...+|++||+|.+.++|.+ +..|||+
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            35778999999  55443        4679999999999999999886544  3456999999999766655 5579999


Q ss_pred             eeCCEEEEEEecCchHH
Q psy6490         314 MIKNKKVECKKAQPKEA  330 (398)
Q Consensus       314 ~i~g~~i~v~~a~~k~~  330 (398)
                      .++||.|.|.++....-
T Consensus        82 ~f~gR~v~v~f~~~~~y   98 (104)
T d1o0pa_          82 KFANRVVVTKYCDPDSY   98 (104)
T ss_dssp             CSSSSCCEEEEECHHHH
T ss_pred             EECCeEEEEEEcCHHHh
Confidence            99999999999876543

>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=99.30  E-value=1.3e-12  Score=97.81  Aligned_cols=78  Identities=15%  Similarity=0.333  Sum_probs=67.1

Q ss_pred             CCcEEEEcCC--CCCCC---------HHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         160 TSAKLFVGGL--SWQTS---------SEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       160 ~~~~l~v~nL--p~~~t---------~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      .+++|+|+||  +.++.         +++|++.|++||.|.+|++..++    .+||+||+|.+.++|.+|++ +++..+
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            6799999999  55432         36789999999999999887664    58999999999999999998 999999


Q ss_pred             CCcccCCCCCCCCC
Q psy6490         228 DGKKIDPKHATPKN  241 (398)
Q Consensus       228 ~g~~l~v~~~~~~~  241 (398)
                      +||.|.+.+...+.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999876543

>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=99.20  E-value=4.6e-12  Score=95.73  Aligned_cols=79  Identities=14%  Similarity=0.160  Sum_probs=67.1

Q ss_pred             CCcEEEEcCC--CCCCC--------HHHHHHHHhcCCCEEEEEEeeCCCCC--CcccEEEEEEcChHhHHHHHh-CCCcc
Q psy6490         160 TSAKLFVGGL--SWQTS--------SEKLREYFGMFGAVTDVLIMKDPITQ--RSRGFGFITFAEPETVEKVLK-VPIHT  226 (398)
Q Consensus       160 ~~~~l~v~nL--p~~~t--------~~~L~~~f~~~G~i~~~~~~~~~~~~--~~~g~afV~f~~~e~a~~al~-~~~~~  226 (398)
                      ++++|.|+||  +.++.        .+||++.|++||.|++|.|.++..+.  ...|++||+|.+.++|.+|++ +++..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            6899999999  55543        35689999999999999998866443  456899999999999999998 99999


Q ss_pred             cCCcccCCCCCC
Q psy6490         227 LDGKKIDPKHAT  238 (398)
Q Consensus       227 ~~g~~l~v~~~~  238 (398)
                      ++||.|.+.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999887754

>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=97.93  E-value=1.4e-05  Score=55.63  Aligned_cols=55  Identities=13%  Similarity=0.181  Sum_probs=49.3

Q ss_pred             HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHCCceeCCEEEEEEecC
Q psy6490         264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       264 e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l~~~~i~g~~i~v~~a~  326 (398)
                      .+|.+.|..||+|.-||++.|        -.+|+|.+-++|.+++++++.++.|+.|+|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEecCC
Confidence            578888999999999998866        6799999999999999999999999999998643

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.45  E-value=0.00019  Score=50.65  Aligned_cols=67  Identities=7%  Similarity=0.125  Sum_probs=53.1

Q ss_pred             cceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHH-HHCCceeC
Q psy6490         250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR--HRGFGFVTFENEEVVDHIC-EIHFHMIK  316 (398)
Q Consensus       250 ~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~--~kg~afV~F~~~eaa~a~~-~l~~~~i~  316 (398)
                      ++|.|+.||..+||+++.+.++..|.+........+.+.+  .-..|||.|.+.++..... ..+|+.+-
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4799999999999999999999999999887776544432  1256999999977776654 68888764

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.45  E-value=0.00057  Score=44.90  Aligned_cols=60  Identities=20%  Similarity=0.174  Sum_probs=47.3

Q ss_pred             HHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH-HHHHCCceeCCEEEEEEecC
Q psy6490         264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQ  326 (398)
Q Consensus       264 e~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a-~~~l~~~~i~g~~i~v~~a~  326 (398)
                      +.|.+.|.++|.|.++.|.... .+  .-.|-|...+..+|.- +-.||..+|++++|.|.++.
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            3455688999999999987653 33  2368999999666654 55799999999999999975

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=0.00029  Score=49.75  Aligned_cols=66  Identities=12%  Similarity=0.095  Sum_probs=53.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCC--cccEEEEEEcChHhHHHHHh-CCCccc
Q psy6490         162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR--SRGFGFITFAEPETVEKVLK-VPIHTL  227 (398)
Q Consensus       162 ~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~--~~g~afV~f~~~e~a~~al~-~~~~~~  227 (398)
                      +.|.|+.||+++||+++.+.++..|++........+.+.+  .-..|||.|.+.++.....+ .++..+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            5799999999999999999999999988887777654433  22459999999999988876 455544

>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=97.27  E-value=9.1e-05  Score=51.45  Aligned_cols=70  Identities=21%  Similarity=0.257  Sum_probs=55.9

Q ss_pred             CCcEEEEcCCCCCC------CH---HHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHhCCCcccCCc
Q psy6490         160 TSAKLFVGGLSWQT------SS---EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGK  230 (398)
Q Consensus       160 ~~~~l~v~nLp~~~------t~---~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~~~~~~~~g~  230 (398)
                      +..||.|.=...+.      +|   .+|.+.|..||+|.-+|++.|        --+|+|.+-++|.+|+++++.++.|+
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~   85 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGR   85 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcce
Confidence            56777775444332      22   457778899999999999877        58999999999999999999999999


Q ss_pred             ccCCCCC
Q psy6490         231 KIDPKHA  237 (398)
Q Consensus       231 ~l~v~~~  237 (398)
                      .|.+...
T Consensus        86 ~l~It~~   92 (95)
T d1ufwa_          86 AVKISGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9877543

>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=96.12  E-value=0.0036  Score=41.01  Aligned_cols=59  Identities=19%  Similarity=0.152  Sum_probs=48.3

Q ss_pred             HHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh-CCCcccCCcccCCCCCC
Q psy6490         177 KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT  238 (398)
Q Consensus       177 ~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~  238 (398)
                      .|.+.|.++|.|.++.+..-. +|  .-.|-|...+..+|..++. ++...+++++|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            355678999999999886542 23  3369999999999999998 89999999999887654

>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=95.90  E-value=0.02  Score=40.07  Aligned_cols=55  Identities=18%  Similarity=0.334  Sum_probs=44.7

Q ss_pred             cccceeecCCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy6490         248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI  310 (398)
Q Consensus       248 ~~~~l~V~nLp~~~tee~L~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~F~~~eaa~a~~~l  310 (398)
                      ....||.-..|..+...||.++|+.||.|. |..+-|  +     -|||...+.|.++.++.+
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHH
Confidence            345588888999999999999999999987 343433  2     799999999998887764

>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=95.86  E-value=0.02  Score=40.09  Aligned_cols=56  Identities=18%  Similarity=0.386  Sum_probs=46.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHhcCCCEEEEEEeeCCCCCCcccEEEEEEcChHhHHHHHh
Q psy6490         158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK  221 (398)
Q Consensus       158 ~~~~~~l~v~nLp~~~t~~~L~~~f~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~a~~al~  221 (398)
                      ......||.-..|..+...||.++|+.||.|.-- .+.|.       .|||...+.|+++.+++
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~Vs-wIddT-------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQIS-WIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCE-EEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEE-EecCc-------eEEEEecCHHHHHHHHH
Confidence            3466788888899999999999999999987633 33442       69999999999988875